sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-06.freexian.com
+==============================================================================+
| lambda-align 1.0.3-6 (arm64) Sat, 23 Nov 2024 10:27:57 +0000 |
+==============================================================================+
Package: lambda-align
Version: 1.0.3-6
Source Version: 1.0.3-6
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: binary
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/1053884/system.tar.xz to /tmp/tmp.sbuild.r8JGpq__Lv...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
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| Chroot Setup Commands |
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rm -f /etc/resolv.conf
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I: Finished running 'rm -f /etc/resolv.conf'.
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Copying /tmp/debusine-fetch-exec-upload-xsvahb1s/seqan-apps-dbgsym_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-xsvahb1s/seqan-apps_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-xsvahb1s/libseqan2-dev_2.5.0~rc3+dfsg-1_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/lambda-align-7zF7r6/resolver-b3TJPy' with '<<RESOLVERDIR>>'
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| Update chroot |
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Get:1 file:/build/lambda-align-7zF7r6/resolver-qH6e5C/apt_archive ./ InRelease
Ign:1 file:/build/lambda-align-7zF7r6/resolver-qH6e5C/apt_archive ./ InRelease
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Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:4 file:/build/lambda-align-7zF7r6/resolver-qH6e5C/apt_archive ./ Release.gpg
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Get:5 file:/build/lambda-align-7zF7r6/resolver-qH6e5C/apt_archive ./ Packages [4687 B]
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Get:7 http://deb.debian.org/debian sid/main arm64 Components [4913 kB]
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Reading package lists...
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Calculating upgrade...
The following packages will be upgraded:
apt base-files libapt-pkg6.0t64 libxml-sax-perl
4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
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Get:3 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.14 [1316 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
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| Fetch source files |
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Local sources
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/tmp/debusine-fetch-exec-upload-xsvahb1s/lambda-align_1.0.3-6.dsc exists in /tmp/debusine-fetch-exec-upload-xsvahb1s; copying to chroot
I: NOTICE: Log filtering will replace 'build/lambda-align-7zF7r6/lambda-align-1.0.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/lambda-align-7zF7r6' with '<<BUILDDIR>>'
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), libseqan2-dev, cmake, zlib1g-dev, libbz2-dev, openssl, build-essential, fakeroot
Filtered Build-Depends: debhelper (>= 12~), libseqan2-dev, cmake, zlib1g-dev, libbz2-dev, openssl, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Install main build dependencies (apt-based resolver)
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Installing build dependencies
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Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev build-essential cmake cmake-data
cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper
dh-autoreconf dh-strip-nondeterminism dwz fakeroot g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libarchive13t64 libasan8
libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4t64
libdebhelper-perl libelf1t64 libexpat1 libfakeroot
libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1
libjsoncpp26 liblsan0 libmpc3 libmpfr6 libncursesw6 libproc2-0 librhash1
libseqan2-dev libstdc++-14-dev libtool libtsan2 libubsan1 libuv1t64
linux-libc-dev m4 po-debconf procps rpcsvc-proto zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build cpp-doc gcc-14-locales cpp-14-doc dh-make
gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
gdb-aarch64-linux-gnu lrzip libc-devtools glibc-doc libstdc++-14-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl
Recommended packages:
bzip2-doc manpages manpages-dev libarchive-cpio-perl libgpm2 libltdl-dev
libmail-sendmail-perl psmisc linux-sysctl-defaults
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential cmake cmake-data
cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper
dh-autoreconf dh-strip-nondeterminism dwz fakeroot g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libarchive13t64 libasan8
libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4t64
libdebhelper-perl libelf1t64 libexpat1 libfakeroot
libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1
libjsoncpp26 liblsan0 libmpc3 libmpfr6 libncursesw6 libproc2-0 librhash1
libseqan2-dev libstdc++-14-dev libtool libtsan2 libubsan1 libuv1t64
linux-libc-dev m4 po-debconf procps rpcsvc-proto
sbuild-build-depends-main-dummy zlib1g-dev
0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded.
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.9-1
Package versions: appstream_1.0.3-1+b1 apt_2.9.14 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.5 bash_5.2.32-1+b2 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 bsdextrautils_2.40.2-11 bsdutils_1:2.40.2-11 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 cmake_3.31.1-1 cmake-data_3.31.1-1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-aarch64-linux-gnu_14.2.0-8 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9+b1 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffstat_1.67-1 diffutils_1:3.10-1+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-8 g++-14-aarch64-linux-gnu_14.2.0-8 g++-aarch64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-8 gcc-14-aarch64-linux-gnu_14.2.0-8 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: lambda-align
Binary: lambda-align
Architecture: any
Version: 1.0.3-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>, Michael R. Crusoe <michael.crusoe@gmail.com>
Homepage: https://seqan.github.io/lambda
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/lambda-align
Vcs-Git: https://salsa.debian.org/med-team/lambda-align.git
Testsuite: autopkgtest
Testsuite-Triggers: @builddeps@, coreutils, diffutils, gzip, openssl
Build-Depends: debhelper (>= 12~), libseqan2-dev, cmake, zlib1g-dev, libbz2-dev, openssl
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gpgv: Signature made Sat Feb 8 15:33:49 2020 UTC
gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./lambda-align_1.0.3-6.dsc: no acceptable signature found
dpkg-source: info: extracting lambda-align in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking lambda-align_1.0.3.orig.tar.gz
dpkg-source: info: unpacking lambda-align_1.0.3-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying set-seqan-cmake-dir.patch
dpkg-source: info: applying force-link-rt-pthread.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package lambda-align
dpkg-buildpackage: info: source version 1.0.3-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sascha Steinbiss <satta@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
fakeroot debian/rules clean
dh clean --builddirectory=build
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.1
dh_auto_clean --
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--builddirectory=build
dh_clean -O--builddirectory=build
debian/rules build
dh build --builddirectory=build
dh_update_autotools_config -O--builddirectory=build
dh_autoreconf -O--builddirectory=build
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON -DCMAKE_BUILD_TYPE=Release
cd build && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON -DCMAKE_BUILD_TYPE=Release ..
CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
[1mCompiler Detection[m
-- The CXX compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
[1mDependency detection[m
-- These dependencies where found:
OPENMP TRUE -fopenmp
ZLIB TRUE 1.3.1
BZIP2 TRUE 1.0.8
SEQAN TRUE 2.5.0
-- The requirements where met.
[1mBuild configuration[m
-- LAMBDA version is: 1.0.2
-- The following options are selected for the build:
LAMBDA_FASTBUILD OFF
LAMBDA_LINGAPS_OPT OFF
LAMBDA_MMAPPED_DB ON
LAMBDA_NATIVE_BUILD OFF
LAMBDA_STATIC_BUILD OFF
-- Run 'cmake -LH' to get a comment on each option.
-- Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option.
[1mSetting up unit tests[m
CMake Deprecation Warning at tests/CMakeLists.txt:5 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Configuring done (2.1s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<PKGBUILDDIR>>/build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -O--builddirectory=build
cd build && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build --check-build-system CMakeFiles/Makefile.cmake 0
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make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/depend
make -f src/CMakeFiles/lambda_indexer.dir/build.make src/CMakeFiles/lambda_indexer.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src /<<PKGBUILDDIR>>/build/src/CMakeFiles/lambda.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src /<<PKGBUILDDIR>>/build/src/CMakeFiles/lambda_indexer.dir/DependInfo.cmake "--color="
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make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/build
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make -f src/CMakeFiles/lambda_indexer.dir/build.make src/CMakeFiles/lambda_indexer.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 50%] Building CXX object src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o
[ 50%] Building CXX object src/CMakeFiles/lambda.dir/lambda.cpp.o
cd /<<PKGBUILDDIR>>/build/src && /usr/bin/c++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.5.0\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-vla -flto=8 -O3 -DNDEBUG -s -fopenmp -MD -MT src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -MF CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o.d -o CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -c /<<PKGBUILDDIR>>/src/lambda_indexer.cpp
cd /<<PKGBUILDDIR>>/build/src && /usr/bin/c++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.5.0\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-vla -flto=8 -O3 -DNDEBUG -s -fopenmp -MD -MT src/CMakeFiles/lambda.dir/lambda.cpp.o -MF CMakeFiles/lambda.dir/lambda.cpp.o.d -o CMakeFiles/lambda.dir/lambda.cpp.o -c /<<PKGBUILDDIR>>/src/lambda.cpp
In file included from /<<PKGBUILDDIR>>/src/lambda.cpp:32:
/<<PKGBUILDDIR>>/src/options.hpp:323:21: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
323 | setDate(parser, __DATE__);
| ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/misc.hpp:34,
from /<<PKGBUILDDIR>>/src/lambda_indexer.hpp:35,
from /<<PKGBUILDDIR>>/src/lambda_indexer.cpp:31:
/<<PKGBUILDDIR>>/src/options.hpp:323:21: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
323 | setDate(parser, __DATE__);
| ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/lambda.cpp:31:
/<<PKGBUILDDIR>>/src/output.hpp:28:17: error: ‘seqan’ is not a namespace-name
28 | using namespace seqan;
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void blastMatchOneCigar(TCigar&, const TBlastMatch&, const TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/output.hpp:112:29: error: expected nested-name-specifier before ‘Value’
112 | using TCElem = typename Value<TCigar>::Type;
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:128:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
128 | appendValue(cigar, TCElem('H', leftFrameClip + leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:128:32: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/<<PKGBUILDDIR>>/src/output.hpp:132:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
132 | appendValue(cigar, TCElem('H', leftFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:134:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
134 | appendValue(cigar, TCElem('S', leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:147:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
147 | appendValue(cigar, TCElem('D', count * transFac));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:157:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
157 | appendValue(cigar, TCElem('I', count * transFac));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:167:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
167 | appendValue(cigar, TCElem('M', count * transFac));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:173:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
173 | appendValue(cigar, TCElem('H', rightFrameClip + rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:177:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
177 | appendValue(cigar, TCElem('S', rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:179:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
179 | appendValue(cigar, TCElem('H', rightFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void blastMatchTwoCigar(TCigar&, TCigar&, const TBlastMatch&, const TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/output.hpp:194:29: error: expected nested-name-specifier before ‘Value’
194 | using TCElem = typename Value<TCigar>::Type;
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:208:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
208 | appendValue(dnaCigar, TCElem('H', leftFrameClip + 3 * leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:210:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
210 | appendValue(protCigar, TCElem('H', leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:215:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
215 | appendValue(dnaCigar, TCElem('H', leftFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:219:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
219 | appendValue(dnaCigar, TCElem('S', 3 * leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:220:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
220 | appendValue(protCigar, TCElem('S', leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:235:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
235 | appendValue(dnaCigar, TCElem('D', count * 3));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:236:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
236 | appendValue(protCigar, TCElem('D', count));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:248:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
248 | appendValue(dnaCigar, TCElem('I', count * 3));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:249:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
249 | appendValue(protCigar, TCElem('I', count));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:261:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
261 | appendValue(dnaCigar, TCElem('M', count * 3));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:262:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
262 | appendValue(protCigar, TCElem('M', count));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:269:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
269 | appendValue(dnaCigar, TCElem('H', rightFrameClip + 3 * rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:271:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
271 | appendValue(protCigar, TCElem('H', rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:277:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
277 | appendValue(dnaCigar, TCElem('S', 3 * rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:278:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
278 | appendValue(protCigar, TCElem('S', rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:282:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
282 | appendValue(dnaCigar, TCElem('H', rightFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void myWriteHeader(TGH&, const TLambdaOptions&)’:
/<<PKGBUILDDIR>>/src/output.hpp:316:35: error: ‘seqan’ has not been declared
316 | auto & context = seqan::context(globalHolder.outfileBam);
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:317:35: error: there are no arguments to ‘contigLengths’ that depend on a template parameter, so a declaration of ‘contigLengths’ must be available [-fpermissive]
317 | auto & subjSeqLengths = contigLengths(context);
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:318:35: error: there are no arguments to ‘contigNames’ that depend on a template parameter, so a declaration of ‘contigNames’ must be available [-fpermissive]
318 | auto & subjIds = contigNames(context);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:342:74: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
342 | std::find(begin(globalHolder.subjIds[i], Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:343:72: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
343 | end(globalHolder.subjIds[i], Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:345:66: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
345 | - begin(globalHolder.subjIds[i], Standard()));
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:347:17: error: ‘BamHeaderRecord’ does not name a type
347 | typedef BamHeaderRecord::TTag TTag;
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:350:9: error: ‘BamHeader’ was not declared in this scope; did you mean ‘seqan2::BamHeader’?
350 | BamHeader header;
| ^~~~~~~~~
| seqan2::BamHeader
In file included from /usr/include/seqan/bam_io.h:60,
from /usr/include/seqan/seq_io/bam_sam.h:39,
from /usr/include/seqan/seq_io.h:55,
from /<<PKGBUILDDIR>>/src/lambda.cpp:27:
/usr/include/seqan/bam_io/bam_header_record.h:192:33: note: ‘seqan2::BamHeader’ declared here
192 | typedef String<BamHeaderRecord> BamHeader;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:352:9: error: ‘BamHeaderRecord’ was not declared in this scope; did you mean ‘seqan2::BamHeaderRecord’?
352 | BamHeaderRecord firstRecord;
| ^~~~~~~~~~~~~~~
| seqan2::BamHeaderRecord
/usr/include/seqan/bam_io/bam_header_record.h:163:7: note: ‘seqan2::BamHeaderRecord’ declared here
163 | class BamHeaderRecord
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:353:9: error: ‘firstRecord’ was not declared in this scope
353 | firstRecord.type = BAM_HEADER_FIRST;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:353:28: error: ‘BAM_HEADER_FIRST’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_FIRST’?
353 | firstRecord.type = BAM_HEADER_FIRST;
| ^~~~~~~~~~~~~~~~
| seqan2::BAM_HEADER_FIRST
/usr/include/seqan/bam_io/bam_header_record.h:76:5: note: ‘seqan2::BAM_HEADER_FIRST’ declared here
76 | BAM_HEADER_FIRST = 0,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:354:39: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
354 | appendValue(firstRecord.tags, TTag("VN", "1.4"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:356:39: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
356 | appendValue(firstRecord.tags, TTag("GO", "query"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:357:21: error: ‘header’ was not declared in this scope
357 | appendValue(header, firstRecord);
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:357:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
357 | appendValue(header, firstRecord);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:362:28: error: expected ‘;’ before ‘pgRecord’
362 | BamHeaderRecord pgRecord;
| ^~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:363:13: error: ‘pgRecord’ was not declared in this scope
363 | pgRecord.type = BAM_HEADER_PROGRAM;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:363:29: error: ‘BAM_HEADER_PROGRAM’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_PROGRAM’?
363 | pgRecord.type = BAM_HEADER_PROGRAM;
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_HEADER_PROGRAM
/usr/include/seqan/bam_io/bam_header_record.h:79:5: note: ‘seqan2::BAM_HEADER_PROGRAM’ declared here
79 | BAM_HEADER_PROGRAM = 3,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:364:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
364 | appendValue(pgRecord.tags, TTag("ID", "lambda"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:365:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
365 | appendValue(pgRecord.tags, TTag("PN", "lambda"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:366:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
366 | appendValue(pgRecord.tags, TTag("VN", SEQAN_APP_VERSION));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:368:13: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
368 | appendValue(header, pgRecord);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:372:24: error: expected ‘;’ before ‘hpRecord0’
372 | BamHeaderRecord hpRecord0;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:373:9: error: ‘hpRecord0’ was not declared in this scope
373 | hpRecord0.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:373:26: error: ‘BAM_HEADER_COMMENT’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_COMMENT’?
373 | hpRecord0.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_HEADER_COMMENT
/usr/include/seqan/bam_io/bam_header_record.h:80:5: note: ‘seqan2::BAM_HEADER_COMMENT’ declared here
80 | BAM_HEADER_COMMENT = 4
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:374:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
374 | appendValue(hpRecord0.tags, TTag("CO", "Lambda is a high performance BLAST compatible local aligner, "
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:376:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
376 | appendValue(header, hpRecord0);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:377:24: error: expected ‘;’ before ‘hpRecord1’
377 | BamHeaderRecord hpRecord1;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:378:9: error: ‘hpRecord1’ was not declared in this scope
378 | hpRecord1.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:379:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
379 | appendValue(hpRecord1.tags, TTag("CO", "SAM/BAM dialect documentation is available here: "
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:381:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
381 | appendValue(header, hpRecord1);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:382:24: error: expected ‘;’ before ‘hpRecord2’
382 | BamHeaderRecord hpRecord2;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:383:9: error: ‘hpRecord2’ was not declared in this scope
383 | hpRecord2.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:384:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
384 | appendValue(hpRecord2.tags, TTag("CO", "If you use any results found by Lambda, please cite "
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:386:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
386 | appendValue(header, hpRecord2);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:389:24: error: expected ‘;’ before ‘tagRecord’
389 | BamHeaderRecord tagRecord;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:390:9: error: ‘tagRecord’ was not declared in this scope
390 | tagRecord.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:392:34: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
392 | for (unsigned i = 0; i < length(SamBamExtraTags<>::keyDescPairs); ++i)
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:402:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
402 | appendValue(tagRecord.tags, TTag("CO", columnHeaders));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:403:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
403 | appendValue(header, tagRecord);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:409:38: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
409 | for (unsigned i = 0; i < length(header); ++i)
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:410:64: error: ‘seqan’ has not been declared
410 | write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:410:105: error: there are no arguments to ‘Sam’ that depend on a template parameter, so a declaration of ‘Sam’ must be available [-fpermissive]
410 | write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
| ^~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void myWriteRecord(TLH&, const TRecord&)’:
/<<PKGBUILDDIR>>/src/output.hpp:438:21: error: ‘BamAlignmentRecord’ was not declared in this scope; did you mean ‘seqan2::BamAlignmentRecord’?
438 | std::vector<BamAlignmentRecord> bamRecords;
| ^~~~~~~~~~~~~~~~~~
| seqan2::BamAlignmentRecord
In file included from /usr/include/seqan/bam_io.h:59:
/usr/include/seqan/bam_io/bam_alignment_record.h:241:7: note: ‘seqan2::BamAlignmentRecord’ declared here
241 | class BamAlignmentRecord : public BamAlignmentRecordCore
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:438:39: error: template argument 1 is invalid
438 | std::vector<BamAlignmentRecord> bamRecords;
| ^
/<<PKGBUILDDIR>>/src/output.hpp:438:39: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/src/output.hpp:439:20: error: request for member ‘resize’ in ‘bamRecords’, which is of non-class type ‘int’
439 | bamRecords.resize(record.matches.size());
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:441:9: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
441 | String<CigarElement<>> protCigar;
| ^~~~~~
| seqan2::String
In file included from /usr/include/seqan/sequence.h:105,
from /<<PKGBUILDDIR>>/src/lambda.cpp:25:
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:441:16: error: ‘CigarElement’ was not declared in this scope; did you mean ‘seqan2::CigarElement’?
441 | String<CigarElement<>> protCigar;
| ^~~~~~~~~~~~
| seqan2::CigarElement
In file included from /usr/include/seqan/bam_io.h:58:
/usr/include/seqan/bam_io/cigar.h:93:8: note: ‘seqan2::CigarElement’ declared here
93 | struct CigarElement
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:441:29: error: expected primary-expression before ‘>>’ token
441 | String<CigarElement<>> protCigar;
| ^~
/<<PKGBUILDDIR>>/src/output.hpp:441:32: error: ‘protCigar’ was not declared in this scope
441 | String<CigarElement<>> protCigar;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:444:42: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
444 | auto mIt = begin(record.matches, Standard());
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:445:28: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-fpermissive]
445 | for (auto & bamR : bamRecords)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:445:28: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-fpermissive]
/<<PKGBUILDDIR>>/src/output.hpp:458:31: error: ‘BAM_FLAG_SECONDARY’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_SECONDARY’?
458 | bamR.flag = BAM_FLAG_SECONDARY; // all are secondary for now
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_FLAG_SECONDARY
/usr/include/seqan/bam_io/bam_alignment_record.h:107:5: note: ‘seqan2::BAM_FLAG_SECONDARY’ declared here
107 | BAM_FLAG_SECONDARY = 0x0100,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:460:32: error: ‘BAM_FLAG_RC’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_RC’?
460 | bamR.flag |= BAM_FLAG_RC;
| ^~~~~~~~~~~
| seqan2::BAM_FLAG_RC
/usr/include/seqan/bam_io/bam_alignment_record.h:103:5: note: ‘seqan2::BAM_FLAG_RC’ declared here
103 | BAM_FLAG_RC = 0x0010,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:463:64: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
463 | std::find(begin(mIt->qId, Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:464:62: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
464 | end(mIt->qId, Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:466:56: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
466 | - begin(mIt->qId, Standard()));
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:473:17: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-fpermissive]
473 | clear(protCigar);
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:475:44: error: ‘BlastProgram’ has not been declared
475 | if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:475:92: error: ‘BlastProgram’ has not been declared
475 | if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:484:44: error: ‘BlastProgram’ has not been declared
484 | if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:484:92: error: ‘BlastProgram’ has not been declared
484 | if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:489:77: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
489 | if ((lH.options.samBamSeq > 1) || (mIt == begin(record.matches, Standard())))
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:501:39: error: ‘BlastProgram’ has not been declared
501 | if (lH.gH.blastProgram == BlastProgram::BLASTN)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:574:44: error: ‘BlastProgram’ has not been declared
574 | if ((lH.gH.blastProgram == BlastProgram::BLASTN) || (!writeSeq))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:593:21: error: there are no arguments to ‘empty’ that depend on a template parameter, so a declaration of ‘empty’ must be available [-fpermissive]
593 | if (empty(protCigar))
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:599:21: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-fpermissive]
599 | clear(protCigarString);
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:600:46: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
600 | for (unsigned i = 0; i < length(protCigar); ++i)
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:602:25: error: there are no arguments to ‘appendNumber’ that depend on a template parameter, so a declaration of ‘appendNumber’ must be available [-fpermissive]
602 | appendNumber(protCigarString, protCigar[i].count);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:603:25: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
603 | appendValue(protCigarString, protCigar[i].operation);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:624:20: error: request for member ‘front’ in ‘bamRecords’, which is of non-class type ‘int’
624 | bamRecords.front().flag -= BAM_FLAG_SECONDARY; // remove BAM_FLAG_SECONDARY for first
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:624:36: error: ‘BAM_FLAG_SECONDARY’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_SECONDARY’?
624 | bamRecords.front().flag -= BAM_FLAG_SECONDARY; // remove BAM_FLAG_SECONDARY for first
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_FLAG_SECONDARY
/usr/include/seqan/bam_io/bam_alignment_record.h:107:5: note: ‘seqan2::BAM_FLAG_SECONDARY’ declared here
107 | BAM_FLAG_SECONDARY = 0x0100,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:628:29: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-fpermissive]
628 | for (auto & r : bamRecords)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:628:29: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-fpermissive]
In file included from /<<PKGBUILDDIR>>/src/lambda_indexer.hpp:34:
/<<PKGBUILDDIR>>/src/output.hpp:28:17: error: ‘seqan’ is not a namespace-name
28 | using namespace seqan;
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void blastMatchOneCigar(TCigar&, const TBlastMatch&, const TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/output.hpp:112:29: error: expected nested-name-specifier before ‘Value’
112 | using TCElem = typename Value<TCigar>::Type;
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:128:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
128 | appendValue(cigar, TCElem('H', leftFrameClip + leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:128:32: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/<<PKGBUILDDIR>>/src/output.hpp:132:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
132 | appendValue(cigar, TCElem('H', leftFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:134:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
134 | appendValue(cigar, TCElem('S', leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:147:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
147 | appendValue(cigar, TCElem('D', count * transFac));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:157:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
157 | appendValue(cigar, TCElem('I', count * transFac));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:167:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
167 | appendValue(cigar, TCElem('M', count * transFac));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:173:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
173 | appendValue(cigar, TCElem('H', rightFrameClip + rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:177:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
177 | appendValue(cigar, TCElem('S', rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:179:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
179 | appendValue(cigar, TCElem('H', rightFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void blastMatchTwoCigar(TCigar&, TCigar&, const TBlastMatch&, const TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/output.hpp:194:29: error: expected nested-name-specifier before ‘Value’
194 | using TCElem = typename Value<TCigar>::Type;
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:208:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
208 | appendValue(dnaCigar, TCElem('H', leftFrameClip + 3 * leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:210:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
210 | appendValue(protCigar, TCElem('H', leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:215:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
215 | appendValue(dnaCigar, TCElem('H', leftFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:219:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
219 | appendValue(dnaCigar, TCElem('S', 3 * leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:220:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
220 | appendValue(protCigar, TCElem('S', leftClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:235:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
235 | appendValue(dnaCigar, TCElem('D', count * 3));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:236:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
236 | appendValue(protCigar, TCElem('D', count));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:248:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
248 | appendValue(dnaCigar, TCElem('I', count * 3));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:249:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
249 | appendValue(protCigar, TCElem('I', count));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:261:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
261 | appendValue(dnaCigar, TCElem('M', count * 3));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:262:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
262 | appendValue(protCigar, TCElem('M', count));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:269:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
269 | appendValue(dnaCigar, TCElem('H', rightFrameClip + 3 * rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:271:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
271 | appendValue(protCigar, TCElem('H', rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:277:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
277 | appendValue(dnaCigar, TCElem('S', 3 * rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:278:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
278 | appendValue(protCigar, TCElem('S', rightClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:282:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-fpermissive]
282 | appendValue(dnaCigar, TCElem('H', rightFrameClip));
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void myWriteHeader(TGH&, const TLambdaOptions&)’:
/<<PKGBUILDDIR>>/src/output.hpp:316:35: error: ‘seqan’ has not been declared
316 | auto & context = seqan::context(globalHolder.outfileBam);
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:317:35: error: there are no arguments to ‘contigLengths’ that depend on a template parameter, so a declaration of ‘contigLengths’ must be available [-fpermissive]
317 | auto & subjSeqLengths = contigLengths(context);
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:318:35: error: there are no arguments to ‘contigNames’ that depend on a template parameter, so a declaration of ‘contigNames’ must be available [-fpermissive]
318 | auto & subjIds = contigNames(context);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:342:74: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
342 | std::find(begin(globalHolder.subjIds[i], Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:343:72: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
343 | end(globalHolder.subjIds[i], Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:345:66: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
345 | - begin(globalHolder.subjIds[i], Standard()));
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:347:17: error: ‘BamHeaderRecord’ does not name a type
347 | typedef BamHeaderRecord::TTag TTag;
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:350:9: error: ‘BamHeader’ was not declared in this scope; did you mean ‘seqan2::BamHeader’?
350 | BamHeader header;
| ^~~~~~~~~
| seqan2::BamHeader
In file included from /usr/include/seqan/bam_io.h:60,
from /usr/include/seqan/seq_io/bam_sam.h:39,
from /usr/include/seqan/seq_io.h:55,
from /<<PKGBUILDDIR>>/src/lambda_indexer.cpp:25:
/usr/include/seqan/bam_io/bam_header_record.h:192:33: note: ‘seqan2::BamHeader’ declared here
192 | typedef String<BamHeaderRecord> BamHeader;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:352:9: error: ‘BamHeaderRecord’ was not declared in this scope; did you mean ‘seqan2::BamHeaderRecord’?
352 | BamHeaderRecord firstRecord;
| ^~~~~~~~~~~~~~~
| seqan2::BamHeaderRecord
/usr/include/seqan/bam_io/bam_header_record.h:163:7: note: ‘seqan2::BamHeaderRecord’ declared here
163 | class BamHeaderRecord
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:353:9: error: ‘firstRecord’ was not declared in this scope
353 | firstRecord.type = BAM_HEADER_FIRST;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:353:28: error: ‘BAM_HEADER_FIRST’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_FIRST’?
353 | firstRecord.type = BAM_HEADER_FIRST;
| ^~~~~~~~~~~~~~~~
| seqan2::BAM_HEADER_FIRST
/usr/include/seqan/bam_io/bam_header_record.h:76:5: note: ‘seqan2::BAM_HEADER_FIRST’ declared here
76 | BAM_HEADER_FIRST = 0,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:354:39: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
354 | appendValue(firstRecord.tags, TTag("VN", "1.4"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:356:39: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
356 | appendValue(firstRecord.tags, TTag("GO", "query"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:357:21: error: ‘header’ was not declared in this scope
357 | appendValue(header, firstRecord);
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:357:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
357 | appendValue(header, firstRecord);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:362:28: error: expected ‘;’ before ‘pgRecord’
362 | BamHeaderRecord pgRecord;
| ^~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:363:13: error: ‘pgRecord’ was not declared in this scope
363 | pgRecord.type = BAM_HEADER_PROGRAM;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:363:29: error: ‘BAM_HEADER_PROGRAM’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_PROGRAM’?
363 | pgRecord.type = BAM_HEADER_PROGRAM;
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_HEADER_PROGRAM
/usr/include/seqan/bam_io/bam_header_record.h:79:5: note: ‘seqan2::BAM_HEADER_PROGRAM’ declared here
79 | BAM_HEADER_PROGRAM = 3,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:364:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
364 | appendValue(pgRecord.tags, TTag("ID", "lambda"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:365:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
365 | appendValue(pgRecord.tags, TTag("PN", "lambda"));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:366:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
366 | appendValue(pgRecord.tags, TTag("VN", SEQAN_APP_VERSION));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:368:13: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
368 | appendValue(header, pgRecord);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:372:24: error: expected ‘;’ before ‘hpRecord0’
372 | BamHeaderRecord hpRecord0;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:373:9: error: ‘hpRecord0’ was not declared in this scope
373 | hpRecord0.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:373:26: error: ‘BAM_HEADER_COMMENT’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_COMMENT’?
373 | hpRecord0.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_HEADER_COMMENT
/usr/include/seqan/bam_io/bam_header_record.h:80:5: note: ‘seqan2::BAM_HEADER_COMMENT’ declared here
80 | BAM_HEADER_COMMENT = 4
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:374:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
374 | appendValue(hpRecord0.tags, TTag("CO", "Lambda is a high performance BLAST compatible local aligner, "
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:376:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
376 | appendValue(header, hpRecord0);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:377:24: error: expected ‘;’ before ‘hpRecord1’
377 | BamHeaderRecord hpRecord1;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:378:9: error: ‘hpRecord1’ was not declared in this scope
378 | hpRecord1.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:379:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
379 | appendValue(hpRecord1.tags, TTag("CO", "SAM/BAM dialect documentation is available here: "
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:381:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
381 | appendValue(header, hpRecord1);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:382:24: error: expected ‘;’ before ‘hpRecord2’
382 | BamHeaderRecord hpRecord2;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:383:9: error: ‘hpRecord2’ was not declared in this scope
383 | hpRecord2.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:384:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
384 | appendValue(hpRecord2.tags, TTag("CO", "If you use any results found by Lambda, please cite "
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:386:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
386 | appendValue(header, hpRecord2);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:389:24: error: expected ‘;’ before ‘tagRecord’
389 | BamHeaderRecord tagRecord;
| ^~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/output.hpp:390:9: error: ‘tagRecord’ was not declared in this scope
390 | tagRecord.type = BAM_HEADER_COMMENT;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:392:34: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
392 | for (unsigned i = 0; i < length(SamBamExtraTags<>::keyDescPairs); ++i)
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:402:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-fpermissive]
402 | appendValue(tagRecord.tags, TTag("CO", columnHeaders));
| ^~~~
/<<PKGBUILDDIR>>/src/output.hpp:403:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
403 | appendValue(header, tagRecord);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:409:38: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
409 | for (unsigned i = 0; i < length(header); ++i)
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:410:64: error: ‘seqan’ has not been declared
410 | write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:410:105: error: there are no arguments to ‘Sam’ that depend on a template parameter, so a declaration of ‘Sam’ must be available [-fpermissive]
410 | write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
| ^~~
/<<PKGBUILDDIR>>/src/output.hpp: In function ‘void myWriteRecord(TLH&, const TRecord&)’:
/<<PKGBUILDDIR>>/src/output.hpp:438:21: error: ‘BamAlignmentRecord’ was not declared in this scope; did you mean ‘seqan2::BamAlignmentRecord’?
438 | std::vector<BamAlignmentRecord> bamRecords;
| ^~~~~~~~~~~~~~~~~~
| seqan2::BamAlignmentRecord
In file included from /usr/include/seqan/bam_io.h:59:
/usr/include/seqan/bam_io/bam_alignment_record.h:241:7: note: ‘seqan2::BamAlignmentRecord’ declared here
241 | class BamAlignmentRecord : public BamAlignmentRecordCore
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:438:39: error: template argument 1 is invalid
438 | std::vector<BamAlignmentRecord> bamRecords;
| ^
/<<PKGBUILDDIR>>/src/output.hpp:438:39: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/src/output.hpp:439:20: error: request for member ‘resize’ in ‘bamRecords’, which is of non-class type ‘int’
439 | bamRecords.resize(record.matches.size());
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:441:9: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
441 | String<CigarElement<>> protCigar;
| ^~~~~~
| seqan2::String
In file included from /usr/include/seqan/sequence.h:105,
from /usr/include/seqan/file.h:58,
from /usr/include/seqan/stream.h:62,
from /usr/include/seqan/arg_parse.h:46,
from /<<PKGBUILDDIR>>/src/lambda_indexer.cpp:24:
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:441:16: error: ‘CigarElement’ was not declared in this scope; did you mean ‘seqan2::CigarElement’?
441 | String<CigarElement<>> protCigar;
| ^~~~~~~~~~~~
| seqan2::CigarElement
In file included from /usr/include/seqan/bam_io.h:58:
/usr/include/seqan/bam_io/cigar.h:93:8: note: ‘seqan2::CigarElement’ declared here
93 | struct CigarElement
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:441:29: error: expected primary-expression before ‘>>’ token
441 | String<CigarElement<>> protCigar;
| ^~
/<<PKGBUILDDIR>>/src/output.hpp:441:32: error: ‘protCigar’ was not declared in this scope
441 | String<CigarElement<>> protCigar;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:444:42: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
444 | auto mIt = begin(record.matches, Standard());
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:445:28: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-fpermissive]
445 | for (auto & bamR : bamRecords)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:445:28: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-fpermissive]
/<<PKGBUILDDIR>>/src/output.hpp:458:31: error: ‘BAM_FLAG_SECONDARY’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_SECONDARY’?
458 | bamR.flag = BAM_FLAG_SECONDARY; // all are secondary for now
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_FLAG_SECONDARY
/usr/include/seqan/bam_io/bam_alignment_record.h:107:5: note: ‘seqan2::BAM_FLAG_SECONDARY’ declared here
107 | BAM_FLAG_SECONDARY = 0x0100,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:460:32: error: ‘BAM_FLAG_RC’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_RC’?
460 | bamR.flag |= BAM_FLAG_RC;
| ^~~~~~~~~~~
| seqan2::BAM_FLAG_RC
/usr/include/seqan/bam_io/bam_alignment_record.h:103:5: note: ‘seqan2::BAM_FLAG_RC’ declared here
103 | BAM_FLAG_RC = 0x0010,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:463:64: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
463 | std::find(begin(mIt->qId, Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:464:62: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
464 | end(mIt->qId, Standard()),
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:466:56: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
466 | - begin(mIt->qId, Standard()));
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:473:17: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-fpermissive]
473 | clear(protCigar);
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:475:44: error: ‘BlastProgram’ has not been declared
475 | if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:475:92: error: ‘BlastProgram’ has not been declared
475 | if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:484:44: error: ‘BlastProgram’ has not been declared
484 | if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:484:92: error: ‘BlastProgram’ has not been declared
484 | if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:489:77: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
489 | if ((lH.options.samBamSeq > 1) || (mIt == begin(record.matches, Standard())))
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:501:39: error: ‘BlastProgram’ has not been declared
501 | if (lH.gH.blastProgram == BlastProgram::BLASTN)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:574:44: error: ‘BlastProgram’ has not been declared
574 | if ((lH.gH.blastProgram == BlastProgram::BLASTN) || (!writeSeq))
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:593:21: error: there are no arguments to ‘empty’ that depend on a template parameter, so a declaration of ‘empty’ must be available [-fpermissive]
593 | if (empty(protCigar))
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:599:21: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-fpermissive]
599 | clear(protCigarString);
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:600:46: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
600 | for (unsigned i = 0; i < length(protCigar); ++i)
| ^~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:602:25: error: there are no arguments to ‘appendNumber’ that depend on a template parameter, so a declaration of ‘appendNumber’ must be available [-fpermissive]
602 | appendNumber(protCigarString, protCigar[i].count);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:603:25: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-fpermissive]
603 | appendValue(protCigarString, protCigar[i].operation);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:624:20: error: request for member ‘front’ in ‘bamRecords’, which is of non-class type ‘int’
624 | bamRecords.front().flag -= BAM_FLAG_SECONDARY; // remove BAM_FLAG_SECONDARY for first
| ^~~~~
/<<PKGBUILDDIR>>/src/output.hpp:624:36: error: ‘BAM_FLAG_SECONDARY’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_SECONDARY’?
624 | bamRecords.front().flag -= BAM_FLAG_SECONDARY; // remove BAM_FLAG_SECONDARY for first
| ^~~~~~~~~~~~~~~~~~
| seqan2::BAM_FLAG_SECONDARY
/usr/include/seqan/bam_io/bam_alignment_record.h:107:5: note: ‘seqan2::BAM_FLAG_SECONDARY’ declared here
107 | BAM_FLAG_SECONDARY = 0x0100,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:628:29: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-fpermissive]
628 | for (auto & r : bamRecords)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/output.hpp:628:29: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-fpermissive]
/<<PKGBUILDDIR>>/src/options.hpp: At global scope:
/<<PKGBUILDDIR>>/src/options.hpp:61:25: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
61 | struct SizeTypePosMeta_<Dna5>
| ^~~~
| seqan2::Dna5
In file included from /usr/include/seqan/basic/basic_alphabet.h:93,
from /usr/include/seqan/basic/basic_container.h:47,
from /usr/include/seqan/basic.h:71,
from /<<PKGBUILDDIR>>/src/lambda_indexer.cpp:22:
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/options.hpp:61:29: error: template argument 1 is invalid
61 | struct SizeTypePosMeta_<Dna5>
| ^
/<<PKGBUILDDIR>>/src/options.hpp:76:8: error: ‘SAValue’ is not a class template
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~~~~
| seqan2::StringSet
In file included from /usr/include/seqan/sequence.h:133:
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:33: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’?
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
In file included from /usr/include/seqan/reduced_aminoacid.h:43,
from /<<PKGBUILDDIR>>/src/lambda_indexer.hpp:32:
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:15: error: expected ‘;’ before ‘,’ token
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:82:8: error: ‘SAValue’ is not a class template
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:82:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:82:26: error: ‘ModifiedString’ was not declared in this scope; did you mean ‘seqan2::ModifiedString’?
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~~~~~~~~~
| seqan2::ModifiedString
In file included from /usr/include/seqan/modifier.h:61,
from /usr/include/seqan/file.h:59:
/usr/include/seqan/modifier/modifier_iterator.h:46:49: note: ‘seqan2::ModifiedString’ declared here
46 | template <typename THost, typename TSpec> class ModifiedString;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:82:41: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:82:15: error: expected ‘;’ before ‘,’ token
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:88:8: error: ‘SAValue’ is not a class template
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:88:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:88:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:88:15: error: expected ‘;’ before ‘,’ token
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:94:8: error: ‘DefaultIndexStringSpec’ is not a class template
94 | struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:94:31: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
94 | struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:94:55: error: expected unqualified-id before ‘>’ token
94 | struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
| ^~
/<<PKGBUILDDIR>>/src/options.hpp:105:8: error: ‘FormattedFileContext’ is not a class template
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:105:29: error: ‘FormattedFile’ was not declared in this scope; did you mean ‘seqan2::FormattedFile’?
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~~~~~~~~~~~
| seqan2::FormattedFile
In file included from /usr/include/seqan/stream.h:111:
/usr/include/seqan/stream/formatted_file.h:213:8: note: ‘seqan2::FormattedFile’ declared here
213 | struct FormattedFile
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:105:43: error: ‘Bam’ was not declared in this scope; did you mean ‘seqan2::Bam’?
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~
| seqan2::Bam
In file included from /usr/include/seqan/bam_io.h:70:
/usr/include/seqan/bam_io/read_bam.h:55:19: note: ‘seqan2::Bam’ declared here
55 | typedef Tag<Bam_> Bam;
| ^~~
/<<PKGBUILDDIR>>/src/options.hpp:105:60: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’?
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~~~~~~~~~~
| seqan2::BlastTabular
In file included from /usr/include/seqan/blast.h:62,
from /<<PKGBUILDDIR>>/src/output.hpp:25:
/usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here
86 | typedef Tag<BlastTabular_> BlastTabular;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:105:28: error: expected ‘;’ before ‘,’ token
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:123:23: error: ‘Alloc’ does not name a type; did you mean ‘alloca’?
123 | using TAlloc = Alloc<>;
| ^~~~~
| alloca
/<<PKGBUILDDIR>>/src/options.hpp:125:23: error: ‘WaveletTree’ does not name a type
125 | using Bwt = WaveletTree<void, WTRDConfig<LengthSum, TAlloc> >;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:126:23: error: ‘Levels’ does not name a type
126 | using Sentinels = Levels<void, LevelsRDConfig<LengthSum, TAlloc> >;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:132:18: error: ‘FMIndex’ does not name a type
132 | using TFMIndex = FMIndex<TSpec, LambdaFMIndexConfig>;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:136:22: error: ‘StringSet’ does not name a type
136 | using TCDStringSet = StringSet<TString, Owner<ConcatDirect<> > >;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:138:11: error: ‘BlastProgram’ has not been declared
138 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:140:45: error: ‘p’ was not declared in this scope
140 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:140:50: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
140 | (p == BlastProgram::BLASTN) ||
| ^~~~~~~~~~~~
| seqan2::BlastProgram
In file included from /usr/include/seqan/blast.h:59:
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:140:64: error: wrong number of template arguments (1, should be 3)
140 | (p == BlastProgram::BLASTN) ||
| ^~~~~~
In file included from /usr/include/c++/14/bits/move.h:37,
from /usr/include/c++/14/bits/exception_ptr.h:41,
from /usr/include/c++/14/exception:166,
from /usr/include/c++/14/ios:41,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /usr/include/seqan/basic/debug_test_system.h:150,
from /usr/include/seqan/basic/basic_debug.h:52,
from /usr/include/seqan/basic.h:49:
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:140:70: error: expected identifier before ‘)’ token
140 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:146:11: error: ‘BlastProgram’ has not been declared
146 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:148:45: error: ‘p’ was not declared in this scope
148 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:148:50: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
148 | (p == BlastProgram::BLASTN) ||
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:148:64: error: wrong number of template arguments (1, should be 3)
148 | (p == BlastProgram::BLASTN) ||
| ^~~~~~
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:148:70: error: expected identifier before ‘)’ token
148 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:154:11: error: ‘BlastProgram’ has not been declared
154 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:46: error: ‘p’ was not declared in this scope
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp: At global scope:
/<<PKGBUILDDIR>>/src/options.hpp:61:25: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
61 | struct SizeTypePosMeta_<Dna5>
| ^~~~
| seqan2::Dna5
In file included from /usr/include/seqan/basic/basic_alphabet.h:93,
from /usr/include/seqan/basic/basic_container.h:47,
from /usr/include/seqan/basic.h:71,
from /<<PKGBUILDDIR>>/src/lambda.cpp:24:
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/options.hpp:61:29: error: template argument 1 is invalid
61 | struct SizeTypePosMeta_<Dna5>
| ^
/<<PKGBUILDDIR>>/src/options.hpp:76:8: error: ‘SAValue’ is not a class template
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:51: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:65: error: wrong number of template arguments (1, should be 3)
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:71: error: expected identifier before ‘)’ token
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:160:11: error: ‘BlastProgram’ has not been declared
160 | template <BlastProgram p, typename TRedAlph_>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~~~~
| seqan2::StringSet
In file included from /usr/include/seqan/sequence.h:133:
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:33: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’?
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
In file included from /usr/include/seqan/reduced_aminoacid.h:43,
from /<<PKGBUILDDIR>>/src/lambda.cpp:28:
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:76:15: error: expected ‘;’ before ‘,’ token
76 | struct SAValue<StringSet<String<ReducedAminoAcid<TSpec1>, TSpec2>, TSpec3> >
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:82:8: error: ‘SAValue’ is not a class template
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:82:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:44: error: ‘p’ was not declared in this scope
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:82:26: error: ‘ModifiedString’ was not declared in this scope; did you mean ‘seqan2::ModifiedString’?
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~~~~~~~~~
| seqan2::ModifiedString
In file included from /usr/include/seqan/modifier.h:61,
from /usr/include/seqan/file.h:59,
from /usr/include/seqan/stream.h:62,
from /usr/include/seqan/arg_parse.h:46,
from /<<PKGBUILDDIR>>/src/lambda.cpp:26:
/usr/include/seqan/modifier/modifier_iterator.h:46:49: note: ‘seqan2::ModifiedString’ declared here
46 | template <typename THost, typename TSpec> class ModifiedString;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:49: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:63: error: wrong number of template arguments (1, should be 3)
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:69: error: expected identifier before ‘)’ token
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:82:41: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:82:15: error: expected ‘;’ before ‘,’ token
82 | struct SAValue<StringSet<ModifiedString<String<TSpec1, TSpec2>, TFunctor>, TSpec3> >
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:88:8: error: ‘SAValue’ is not a class template
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:88:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:88:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:88:15: error: expected ‘;’ before ‘,’ token
88 | struct SAValue<StringSet<String<TSpec1, TSpec2>, TSpec3> >
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:94:8: error: ‘DefaultIndexStringSpec’ is not a class template
94 | struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:94:31: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
94 | struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:94:55: error: expected unqualified-id before ‘>’ token
94 | struct DefaultIndexStringSpec<StringSet<TString, TSpec>>
| ^~
/<<PKGBUILDDIR>>/src/options.hpp:105:8: error: ‘FormattedFileContext’ is not a class template
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:105:29: error: ‘FormattedFile’ was not declared in this scope; did you mean ‘seqan2::FormattedFile’?
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~~~~~~~~~~~
| seqan2::FormattedFile
In file included from /usr/include/seqan/stream.h:111:
/usr/include/seqan/stream/formatted_file.h:213:8: note: ‘seqan2::FormattedFile’ declared here
213 | struct FormattedFile
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:105:43: error: ‘Bam’ was not declared in this scope; did you mean ‘seqan2::Bam’?
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~
| seqan2::Bam
In file included from /usr/include/seqan/bam_io.h:70:
/usr/include/seqan/bam_io/read_bam.h:55:19: note: ‘seqan2::Bam’ declared here
55 | typedef Tag<Bam_> Bam;
| ^~~
/<<PKGBUILDDIR>>/src/options.hpp:105:60: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’?
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^~~~~~~~~~~~
| seqan2::BlastTabular
In file included from /usr/include/seqan/blast.h:62,
from /<<PKGBUILDDIR>>/src/output.hpp:25:
/usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here
86 | typedef Tag<BlastTabular_> BlastTabular;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:105:28: error: expected ‘;’ before ‘,’ token
105 | struct FormattedFileContext<FormattedFile<Bam, TDirection, BlastTabular>, TStorageSpec>
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:216:5: error: ‘GeneticCodeSpec’ does not name a type
216 | GeneticCodeSpec geneticCode = CANONICAL;
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:121:23: error: ‘MMap’ does not name a type
121 | using TAlloc = MMap<>;
| ^~~~
/<<PKGBUILDDIR>>/src/options.hpp:218:5: error: ‘BlastProgram’ does not name a type
218 | BlastProgram blastProgram = BlastProgram::BLASTX;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp: In constructor ‘SharedOptions::SharedOptions()’:
/<<PKGBUILDDIR>>/src/options.hpp:227:18: error: ‘isTerminal’ was not declared in this scope; did you mean ‘seqan2::isTerminal’?
227 | isTerm = isTerminal();
| ^~~~~~~~~~
| seqan2::isTerminal
In file included from /usr/include/seqan/arg_parse/tool_doc.h:40,
from /usr/include/seqan/arg_parse.h:65:
/usr/include/seqan/misc/terminal.h:98:13: note: ‘seqan2::isTerminal’ declared here
98 | inline bool isTerminal()
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:125:23: error: ‘WaveletTree’ does not name a type
125 | using Bwt = WaveletTree<void, WTRDConfig<LengthSum, TAlloc> >;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:231:13: error: ‘getTerminalSize’ was not declared in this scope; did you mean ‘seqan2::getTerminalSize’?
231 | getTerminalSize(terminalCols, _rows);
| ^~~~~~~~~~~~~~~
| seqan2::getTerminalSize
/usr/include/seqan/misc/terminal.h:196:13: note: ‘seqan2::getTerminalSize’ declared here
196 | inline bool getTerminalSize(unsigned & cols, unsigned & rows)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp: At global scope:
/<<PKGBUILDDIR>>/src/options.hpp:245:17: error: ‘BlastMatchField’ was not declared in this scope; did you mean ‘seqan2::BlastMatchField’?
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^~~~~~~~~~~~~~~
| seqan2::BlastMatchField
/usr/include/seqan/blast/blast_tabular.h:295:8: note: ‘seqan2::BlastMatchField’ declared here
295 | struct BlastMatchField
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:245:33: error: template argument 1 is invalid
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^
/<<PKGBUILDDIR>>/src/options.hpp:245:33: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/src/options.hpp:245:36: error: expected ‘;’ at end of member declaration
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^~~~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:245:40: error: expected unqualified-id before ‘>’ token
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^
/<<PKGBUILDDIR>>/src/options.hpp:126:23: error: ‘Levels’ does not name a type
126 | using Sentinels = Levels<void, LevelsRDConfig<LengthSum, TAlloc> >;
| ^~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:317:1: error: variable or field ‘sharedSetup’ declared void
317 | sharedSetup(ArgumentParser & parser)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:132:18: error: ‘FMIndex’ does not name a type
132 | using TFMIndex = FMIndex<TSpec, LambdaFMIndexConfig>;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:317:13: error: ‘ArgumentParser’ was not declared in this scope; did you mean ‘seqan2::ArgumentParser’?
317 | sharedSetup(ArgumentParser & parser)
| ^~~~~~~~~~~~~~
| seqan2::ArgumentParser
In file included from /usr/include/seqan/arg_parse.h:71:
/usr/include/seqan/arg_parse/argument_parser.h:152:7: note: ‘seqan2::ArgumentParser’ declared here
152 | class ArgumentParser
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:136:22: error: ‘StringSet’ does not name a type
136 | using TCDStringSet = StringSet<TString, Owner<ConcatDirect<> > >;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:138:11: error: ‘BlastProgram’ has not been declared
138 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:317:30: error: ‘parser’ was not declared in this scope; did you mean ‘pause’?
317 | sharedSetup(ArgumentParser & parser)
| ^~~~~~
| pause
/<<PKGBUILDDIR>>/src/options.hpp:140:45: error: ‘p’ was not declared in this scope
140 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:140:50: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
140 | (p == BlastProgram::BLASTN) ||
| ^~~~~~~~~~~~
| seqan2::BlastProgram
In file included from /usr/include/seqan/blast.h:59:
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:140:64: error: wrong number of template arguments (1, should be 3)
140 | (p == BlastProgram::BLASTN) ||
| ^~~~~~
In file included from /usr/include/c++/14/bits/move.h:37,
from /usr/include/c++/14/bits/exception_ptr.h:41,
from /usr/include/c++/14/exception:166,
from /usr/include/c++/14/ios:41,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/src/lambda.cpp:22:
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:140:70: error: expected identifier before ‘)’ token
140 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:146:11: error: ‘BlastProgram’ has not been declared
146 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:394:1: error: ‘ArgumentParser’ does not name a type
394 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:148:45: error: ‘p’ was not declared in this scope
148 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:148:50: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
148 | (p == BlastProgram::BLASTN) ||
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:148:64: error: wrong number of template arguments (1, should be 3)
148 | (p == BlastProgram::BLASTN) ||
| ^~~~~~
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:148:70: error: expected identifier before ‘)’ token
148 | (p == BlastProgram::BLASTN) ||
| ^
/<<PKGBUILDDIR>>/src/options.hpp:154:11: error: ‘BlastProgram’ has not been declared
154 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:397:1: error: ‘ArgumentParser’ does not name a type
397 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:46: error: ‘p’ was not declared in this scope
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:155:51: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:65: error: wrong number of template arguments (1, should be 3)
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:155:71: error: expected identifier before ‘)’ token
155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:160:11: error: ‘BlastProgram’ has not been declared
160 | template <BlastProgram p, typename TRedAlph_>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1030:1: error: ‘ArgumentParser’ does not name a type
1030 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:44: error: ‘p’ was not declared in this scope
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:161:49: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:63: error: wrong number of template arguments (1, should be 3)
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^~~~~~
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:161:69: error: expected identifier before ‘)’ token
161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN),
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1211:1: error: ‘ArgumentParser’ does not name a type
1211 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:216:5: error: ‘GeneticCodeSpec’ does not name a type
216 | GeneticCodeSpec geneticCode = CANONICAL;
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:11: error: ‘AminoAcid’ was not declared in this scope; did you mean ‘seqan2::AminoAcid’?
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
| seqan2::AminoAcid
/usr/include/seqan/basic/alphabet_residue.h:550:47: note: ‘seqan2::AminoAcid’ declared here
550 | typedef SimpleType<unsigned char, AminoAcid_> AminoAcid;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:1: error: redefinition of ‘constexpr const char* const _alphName’
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:11: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’?
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:28: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’?
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~~~~
| seqan2::Murphy10
In file included from /usr/include/seqan/reduced_aminoacid.h:57:
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here
85 | typedef Tag<Murphy10_> Murphy10;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:38: error: expected primary-expression before ‘const’
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1310:1: error: redefinition of ‘constexpr const char* const _alphName’
1310 | _alphName(Dna const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:218:5: error: ‘BlastProgram’ does not name a type
218 | BlastProgram blastProgram = BlastProgram::BLASTX;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1310:11: error: ‘Dna’ was not declared in this scope; did you mean ‘seqan2::Dna’?
1310 | _alphName(Dna const & /**/)
| ^~~
| seqan2::Dna
/usr/include/seqan/basic/alphabet_residue.h:94:41: note: ‘seqan2::Dna’ declared here
94 | typedef SimpleType<unsigned char, Dna_> Dna;
| ^~~
/<<PKGBUILDDIR>>/src/options.hpp:1316:1: error: redefinition of ‘constexpr const char* const _alphName’
1316 | _alphName(Dna5 const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1316:11: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
1316 | _alphName(Dna5 const & /**/)
| ^~~~
| seqan2::Dna5
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/options.hpp: In constructor ‘SharedOptions::SharedOptions()’:
/<<PKGBUILDDIR>>/src/options.hpp:227:18: error: ‘isTerminal’ was not declared in this scope; did you mean ‘seqan2::isTerminal’?
227 | isTerm = isTerminal();
| ^~~~~~~~~~
| seqan2::isTerminal
In file included from /usr/include/seqan/arg_parse/tool_doc.h:40,
from /usr/include/seqan/arg_parse.h:65:
/usr/include/seqan/misc/terminal.h:98:13: note: ‘seqan2::isTerminal’ declared here
98 | inline bool isTerminal()
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:231:13: error: ‘getTerminalSize’ was not declared in this scope; did you mean ‘seqan2::getTerminalSize’?
231 | getTerminalSize(terminalCols, _rows);
| ^~~~~~~~~~~~~~~
| seqan2::getTerminalSize
/usr/include/seqan/misc/terminal.h:196:13: note: ‘seqan2::getTerminalSize’ declared here
196 | inline bool getTerminalSize(unsigned & cols, unsigned & rows)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp: In function ‘void printOptions(const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/options.hpp:1362:41: error: ‘BlastProgram’ has not been declared
1362 | << ((TGH::blastProgram != BlastProgram::BLASTN) &&
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1363:41: error: ‘BlastProgram’ has not been declared
1363 | (TGH::blastProgram != BlastProgram::BLASTP)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1364:43: error: ‘const struct LambdaOptions’ has no member named ‘geneticCode’
1364 | ? std::to_string(options.geneticCode)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp: At global scope:
/<<PKGBUILDDIR>>/src/options.hpp:245:17: error: ‘BlastMatchField’ was not declared in this scope; did you mean ‘seqan2::BlastMatchField’?
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^~~~~~~~~~~~~~~
| seqan2::BlastMatchField
/usr/include/seqan/blast/blast_tabular.h:295:8: note: ‘seqan2::BlastMatchField’ declared here
295 | struct BlastMatchField
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:245:33: error: template argument 1 is invalid
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^
/<<PKGBUILDDIR>>/src/options.hpp:245:33: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/src/options.hpp:245:36: error: expected ‘;’ at end of member declaration
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^~~~
| ;
/<<PKGBUILDDIR>>/src/options.hpp:245:40: error: expected unqualified-id before ‘>’ token
245 | std::vector<BlastMatchField<>::Enum> columns;
| ^
/<<PKGBUILDDIR>>/src/options.hpp:317:1: error: variable or field ‘sharedSetup’ declared void
317 | sharedSetup(ArgumentParser & parser)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:317:13: error: ‘ArgumentParser’ was not declared in this scope; did you mean ‘seqan2::ArgumentParser’?
317 | sharedSetup(ArgumentParser & parser)
| ^~~~~~~~~~~~~~
| seqan2::ArgumentParser
In file included from /usr/include/seqan/arg_parse.h:71:
/usr/include/seqan/arg_parse/argument_parser.h:152:7: note: ‘seqan2::ArgumentParser’ declared here
152 | class ArgumentParser
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1368:62: error: ‘OrigQryAlph’ was not declared in this scope
1368 | << " original alphabet (query):" << _alphName(OrigQryAlph<TGH::blastProgram>())
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1368:93: error: expected primary-expression before ‘)’ token
1368 | << " original alphabet (query):" << _alphName(OrigQryAlph<TGH::blastProgram>())
| ^
/<<PKGBUILDDIR>>/src/options.hpp:317:30: error: ‘parser’ was not declared in this scope; did you mean ‘pause’?
317 | sharedSetup(ArgumentParser & parser)
| ^~~~~~
| pause
/<<PKGBUILDDIR>>/src/options.hpp:394:1: error: ‘ArgumentParser’ does not name a type
394 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1370:62: error: ‘OrigSubjAlph’ was not declared in this scope
1370 | << " original alphabet (subj): " << _alphName(OrigSubjAlph<TGH::blastProgram>())
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1370:94: error: expected primary-expression before ‘)’ token
1370 | << " original alphabet (subj): " << _alphName(OrigSubjAlph<TGH::blastProgram>())
| ^
/<<PKGBUILDDIR>>/src/options.hpp:397:1: error: ‘ArgumentParser’ does not name a type
397 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1372:62: error: ‘TransAlph’ was not declared in this scope
1372 | << " translated alphabet: " << _alphName(TransAlph<TGH::blastProgram>())
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1372:91: error: expected primary-expression before ‘)’ token
1372 | << " translated alphabet: " << _alphName(TransAlph<TGH::blastProgram>())
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1030:1: error: ‘ArgumentParser’ does not name a type
1030 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp: At global scope:
/<<PKGBUILDDIR>>/src/misc.hpp:80:18: error: ‘Iter’ does not name a type
80 | const Iter<const String<SimpleType<unsigned char,TAlph>,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:80:22: error: expected ‘,’ or ‘...’ before ‘<’ token
80 | const Iter<const String<SimpleType<unsigned char,TAlph>,
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1211:1: error: ‘ArgumentParser’ does not name a type
1211 | ArgumentParser::ParseResult
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp: In function ‘std::basic_ostream<char>& operator<<(std::basic_ostream<char>&, int)’:
/<<PKGBUILDDIR>>/src/misc.hpp:84:13: error: ‘it’ was not declared in this scope; did you mean ‘int’?
84 | out << *it;
| ^~
| int
/<<PKGBUILDDIR>>/src/options.hpp:1280:11: error: ‘AminoAcid’ was not declared in this scope; did you mean ‘seqan2::AminoAcid’?
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
| seqan2::AminoAcid
/usr/include/seqan/basic/alphabet_residue.h:550:47: note: ‘seqan2::AminoAcid’ declared here
550 | typedef SimpleType<unsigned char, AminoAcid_> AminoAcid;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:1: error: redefinition of ‘constexpr const char* const _alphName’
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp: At global scope:
/<<PKGBUILDDIR>>/src/misc.hpp:145:17: error: ‘Gaps’ was not declared in this scope; did you mean ‘seqan2::Gaps’?
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^~~~
| seqan2::Gaps
In file included from /usr/include/seqan/align.h:82,
from /usr/include/seqan/bam_io.h:50:
/usr/include/seqan/align/gaps_base.h:144:7: note: ‘seqan2::Gaps’ declared here
144 | class Gaps;
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:145:30: error: expected primary-expression before ‘,’ token
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:145:42: error: expected primary-expression before ‘>’ token
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1286:11: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’?
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:28: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’?
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~~~~
| seqan2::Murphy10
In file included from /usr/include/seqan/reduced_aminoacid.h:57:
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here
85 | typedef Tag<Murphy10_> Murphy10;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1286:38: error: expected primary-expression before ‘const’
1286 | _alphName(ReducedAminoAcid<Murphy10> const & /**/)
| ^~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1310:1: error: redefinition of ‘constexpr const char* const _alphName’
1310 | _alphName(Dna const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1310:11: error: ‘Dna’ was not declared in this scope; did you mean ‘seqan2::Dna’?
1310 | _alphName(Dna const & /**/)
| ^~~
| seqan2::Dna
/usr/include/seqan/basic/alphabet_residue.h:94:41: note: ‘seqan2::Dna’ declared here
94 | typedef SimpleType<unsigned char, Dna_> Dna;
| ^~~
/<<PKGBUILDDIR>>/src/options.hpp:1316:1: error: redefinition of ‘constexpr const char* const _alphName’
1316 | _alphName(Dna5 const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here
1280 | _alphName(AminoAcid const & /**/)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1316:11: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
1316 | _alphName(Dna5 const & /**/)
| ^~~~
| seqan2::Dna5
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:145:46: error: ‘row0’ was not declared in this scope
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:146:17: error: ‘Gaps’ was not declared in this scope; did you mean ‘seqan2::Gaps’?
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^~~~
| seqan2::Gaps
/<<PKGBUILDDIR>>/src/options.hpp: In function ‘void printOptions(const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/options.hpp:1362:41: error: ‘BlastProgram’ has not been declared
1362 | << ((TGH::blastProgram != BlastProgram::BLASTN) &&
| ^~~~~~~~~~~~
/usr/include/seqan/align/gaps_base.h:144:7: note: ‘seqan2::Gaps’ declared here
144 | class Gaps;
| ^~~~
/<<PKGBUILDDIR>>/src/options.hpp:1363:41: error: ‘BlastProgram’ has not been declared
1363 | (TGH::blastProgram != BlastProgram::BLASTP)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:146:30: error: expected primary-expression before ‘,’ token
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:146:42: error: expected primary-expression before ‘>’ token
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1364:43: error: ‘const struct LambdaOptions’ has no member named ‘geneticCode’
1364 | ? std::to_string(options.geneticCode)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:146:46: error: ‘row1’ was not declared in this scope
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:147:17: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^~~~~
| seqan2::Score
In file included from /usr/include/seqan/score.h:45,
from /usr/include/seqan/graph_align.h:45,
from /usr/include/seqan/align.h:59:
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:147:34: error: expected primary-expression before ‘,’ token
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:147:46: error: expected primary-expression before ‘>’ token
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:147:48: error: expected primary-expression before ‘const’
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:148:17: error: expected primary-expression before ‘int’
148 | int const lowerDiag,
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:149:17: error: expected primary-expression before ‘int’
149 | int const upperDiag,
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:150:31: error: expected primary-expression before ‘&’ token
150 | TAlignContext & alignContext)
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1368:62: error: ‘OrigQryAlph’ was not declared in this scope
1368 | << " original alphabet (query):" << _alphName(OrigQryAlph<TGH::blastProgram>())
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1368:93: error: expected primary-expression before ‘)’ token
1368 | << " original alphabet (query):" << _alphName(OrigQryAlph<TGH::blastProgram>())
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:150:33: error: ‘alignContext’ was not declared in this scope; did you mean ‘TAlignContext’?
150 | TAlignContext & alignContext)
| ^~~~~~~~~~~~
| TAlignContext
/<<PKGBUILDDIR>>/src/misc.hpp:150:46: error: expected ‘;’ before ‘{’ token
150 | TAlignContext & alignContext)
| ^
| ;
151 | {
| ~
/<<PKGBUILDDIR>>/src/misc.hpp:187:1: error: variable or field ‘readRecords’ declared void
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:13: error: ‘TCDStringSet’ was not declared in this scope; did you mean ‘TSeqStringSet’?
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~~~~~~~~
| TSeqStringSet
/<<PKGBUILDDIR>>/src/misc.hpp:187:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:33: error: expected primary-expression before ‘char’
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:39: error: ‘Alloc’ was not declared in this scope; did you mean ‘seqan2::Alloc’?
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~
| seqan2::Alloc
/usr/include/seqan/sequence/string_base.h:59:8: note: ‘seqan2::Alloc’ declared here
59 | struct Alloc {};
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:54: error: expected primary-expression before ‘>>’ token
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:187:56: error: expected primary-expression before ‘>’ token
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^
/<<PKGBUILDDIR>>/src/options.hpp:1370:62: error: ‘OrigSubjAlph’ was not declared in this scope
1370 | << " original alphabet (subj): " << _alphName(OrigSubjAlph<TGH::blastProgram>())
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1370:94: error: expected primary-expression before ‘)’ token
1370 | << " original alphabet (subj): " << _alphName(OrigSubjAlph<TGH::blastProgram>())
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:187:60: error: ‘meta’ was not declared in this scope
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:188:27: error: expected primary-expression before ‘&’ token
188 | TSeqStringSet & seq,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:188:29: error: ‘seq’ was not declared in this scope; did you mean ‘__pstl::execution::v1::seq’?
188 | TSeqStringSet & seq,
| ^~~
| __pstl::execution::v1::seq
In file included from /usr/include/c++/14/pstl/glue_algorithm_defs.h:15,
from /usr/include/c++/14/algorithm:86,
from /usr/include/seqan/basic/debug_test_system.h:156:
/usr/include/c++/14/pstl/execution_defs.h:42:46: note: ‘__pstl::execution::v1::seq’ declared here
42 | _GLIBCXX17_INLINE constexpr sequenced_policy seq{};
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:13: error: ‘FormattedFile’ was not declared in this scope; did you mean ‘seqan2::FormattedFile’?
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~~~~~~~~~~
| seqan2::FormattedFile
/usr/include/seqan/stream/formatted_file.h:213:8: note: ‘seqan2::FormattedFile’ declared here
213 | struct FormattedFile
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:27: error: ‘Fastq’ was not declared in this scope; did you mean ‘seqan2::Fastq’?
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~~
| seqan2::Fastq
In file included from /usr/include/seqan/seq_io.h:52:
/usr/include/seqan/seq_io/fasta_fastq.h:59:24: note: ‘seqan2::Fastq’ declared here
59 | typedef Tag<TagFastq_> Fastq;
| ^~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1372:62: error: ‘TransAlph’ was not declared in this scope
1372 | << " translated alphabet: " << _alphName(TransAlph<TGH::blastProgram>())
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/options.hpp:1372:91: error: expected primary-expression before ‘)’ token
1372 | << " translated alphabet: " << _alphName(TransAlph<TGH::blastProgram>())
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:189:34: error: ‘Input’ was not declared in this scope; did you mean ‘seqan2::Input’?
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~~
| seqan2::Input
In file included from /usr/include/seqan/file.h:71:
/usr/include/seqan/file/file_interface.h:165:21: note: ‘seqan2::Input’ declared here
165 | typedef Tag<Input_> Input;
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:46: error: expected primary-expression before ‘>’ token
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:189:50: error: ‘file’ was not declared in this scope
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:190:19: error: expected primary-expression before ‘maxRecords’
190 | TSize maxRecords)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:15: error: ‘TCDStringSet’ was not declared in this scope
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:35: error: expected primary-expression before ‘char’
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:47: error: expected primary-expression before ‘>>’ token
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:231:52: error: ‘ids’ was not declared in this scope
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:15: error: ‘TCDStringSet’ was not declared in this scope
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:35: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~
| seqan2::Dna5
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:47: error: expected primary-expression before ‘>>’ token
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:232:52: error: ‘seqs’ was not declared in this scope
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:233:51: error: expected primary-expression before ‘&’ token
233 | TFile & file)
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:233:53: error: ‘file’ was not declared in this scope
233 | TFile & file)
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:233:57: error: expression list treated as compound expression in initializer [-fpermissive]
233 | TFile & file)
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:233:58: error: expected ‘;’ before ‘{’ token
233 | TFile & file)
| ^
| ;
234 | {
| ~
/<<PKGBUILDDIR>>/src/misc.hpp:258:1: error: redefinition of ‘template<class TSpec1, class TSpec2, class TFile> int myReadRecords’
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:1: note: ‘template<class TSpec1, class TSpec2, class TFile> int myReadRecords<TSpec1, TSpec2, TFile>’ previously declared here
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:15: error: ‘TCDStringSet’ was not declared in this scope
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:35: error: expected primary-expression before ‘char’
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:47: error: expected primary-expression before ‘>>’ token
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:258:58: error: ‘ids’ was not declared in this scope
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:15: error: ‘TCDStringSet’ was not declared in this scope
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:35: error: ‘AminoAcid’ was not declared in this scope; did you mean ‘seqan2::AminoAcid’?
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~~~~~~
| seqan2::AminoAcid
/usr/include/seqan/basic/alphabet_residue.h:550:47: note: ‘seqan2::AminoAcid’ declared here
550 | typedef SimpleType<unsigned char, AminoAcid_> AminoAcid;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:52: error: expected primary-expression before ‘>>’ token
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:259:58: error: ‘seqs’ was not declared in this scope
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:260:57: error: expected primary-expression before ‘&’ token
260 | TFile & file)
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:260:59: error: ‘file’ was not declared in this scope
260 | TFile & file)
| ^~~~
In file included from /<<PKGBUILDDIR>>/src/lambda_indexer.hpp:37:
/<<PKGBUILDDIR>>/src/radix_inplace.h:66:8: error: ‘Fibre’ is not a class template
66 | struct Fibre<Index<TText, IndexSa<RadixSortSACreateTag > >, FibreTempSA>
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:66:14: error: ‘Index’ was not declared in this scope; did you mean ‘seqan2::Index’?
66 | struct Fibre<Index<TText, IndexSa<RadixSortSACreateTag > >, FibreTempSA>
| ^~~~~
| seqan2::Index
In file included from /usr/include/seqan/index.h:76,
from /<<PKGBUILDDIR>>/src/lambda_indexer.hpp:29:
/usr/include/seqan/index/index_base.h:228:11: note: ‘seqan2::Index’ declared here
228 | class Index;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:66:27: error: ‘IndexSa’ was not declared in this scope; did you mean ‘seqan2::IndexSa’?
66 | struct Fibre<Index<TText, IndexSa<RadixSortSACreateTag > >, FibreTempSA>
| ^~~~~~~
| seqan2::IndexSa
In file included from /usr/include/seqan/index.h:142:
/usr/include/seqan/index/index_sa_stree.h:58:8: note: ‘seqan2::IndexSa’ declared here
58 | struct IndexSa {};
| ^~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:66:13: error: expected ‘;’ before ‘,’ token
66 | struct Fibre<Index<TText, IndexSa<RadixSortSACreateTag > >, FibreTempSA>
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:75:8: error: ‘DefaultIndexCreator’ is not a class template
75 | struct DefaultIndexCreator<Index<TText, IndexSa<RadixSortSACreateTag> >, FibreSA>
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:75:28: error: ‘Index’ was not declared in this scope; did you mean ‘seqan2::Index’?
75 | struct DefaultIndexCreator<Index<TText, IndexSa<RadixSortSACreateTag> >, FibreSA>
| ^~~~~
| seqan2::Index
/usr/include/seqan/index/index_base.h:228:11: note: ‘seqan2::Index’ declared here
228 | class Index;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:75:41: error: ‘IndexSa’ was not declared in this scope; did you mean ‘seqan2::IndexSa’?
75 | struct DefaultIndexCreator<Index<TText, IndexSa<RadixSortSACreateTag> >, FibreSA>
| ^~~~~~~
| seqan2::IndexSa
/usr/include/seqan/index/index_sa_stree.h:58:8: note: ‘seqan2::IndexSa’ declared here
58 | struct IndexSa {};
| ^~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:75:27: error: expected ‘;’ before ‘,’ token
75 | struct DefaultIndexCreator<Index<TText, IndexSa<RadixSortSACreateTag> >, FibreSA>
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:81:8: error: ‘Fibre’ is not a class template
81 | struct Fibre<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreTempSA>
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:81:14: error: ‘Index’ was not declared in this scope; did you mean ‘seqan2::Index’?
81 | struct Fibre<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreTempSA>
| ^~~~~
| seqan2::Index
/usr/include/seqan/index/index_base.h:228:11: note: ‘seqan2::Index’ declared here
228 | class Index;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:81:27: error: ‘FMIndex’ was not declared in this scope; did you mean ‘seqan2::FMIndex’?
81 | struct Fibre<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreTempSA>
| ^~~~~~~
| seqan2::FMIndex
In file included from /usr/include/seqan/index.h:171:
/usr/include/seqan/index/index_fm.h:143:7: note: ‘seqan2::FMIndex’ declared here
143 | class FMIndex;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:81:13: error: expected ‘;’ before ‘,’ token
81 | struct Fibre<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreTempSA>
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:90:8: error: ‘DefaultIndexCreator’ is not a class template
90 | struct DefaultIndexCreator<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreSA>
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:90:28: error: ‘Index’ was not declared in this scope; did you mean ‘seqan2::Index’?
90 | struct DefaultIndexCreator<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreSA>
| ^~~~~
| seqan2::Index
/usr/include/seqan/index/index_base.h:228:11: note: ‘seqan2::Index’ declared here
228 | class Index;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:90:41: error: ‘FMIndex’ was not declared in this scope; did you mean ‘seqan2::FMIndex’?
90 | struct DefaultIndexCreator<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreSA>
| ^~~~~~~
| seqan2::FMIndex
/usr/include/seqan/index/index_fm.h:143:7: note: ‘seqan2::FMIndex’ declared here
143 | class FMIndex;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:90:27: error: expected ‘;’ before ‘,’ token
90 | struct DefaultIndexCreator<Index<TText, FMIndex<RadixSortSACreateTag, TConfig> >, FibreSA>
| ^ ~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:121:17: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
121 | public std::unary_function<TSAValue, TSize>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44:
/usr/include/c++/14/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:124:14: error: expected nested-name-specifier before ‘Size’
124 | typename Size<TString>::Type const L;
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:124:14: error: expected ‘;’ at end of member declaration
124 | typename Size<TString>::Type const L;
| ^~~~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:124:18: error: expected unqualified-id before ‘<’ token
124 | typename Size<TString>::Type const L;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h: In constructor ‘seqan::RadixTextAccessor<TSAValue, TString, void, TSize>::RadixTextAccessor(const TString&)’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:126:56: error: class ‘seqan::RadixTextAccessor<TSAValue, TString, void, TSize>’ does not have any field named ‘L’
126 | RadixTextAccessor(TString const &str) : text(str), L(length(str))
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h: In member function ‘TSize seqan::RadixTextAccessor<TSAValue, TString, void, TSize>::operator()(const TSAValue&, TSize2) const’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:132:18: error: expected nested-name-specifier before ‘Size’
132 | typename Size<TString>::Type pos = x + depth;
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:132:18: error: expected ‘(’ before ‘Size’
/<<PKGBUILDDIR>>/src/radix_inplace.h:133:13: error: ‘pos’ was not declared in this scope; did you mean ‘pow’?
133 | if (pos >= L) return 0;
| ^~~
| pow
/<<PKGBUILDDIR>>/src/radix_inplace.h:133:20: error: ‘L’ was not declared in this scope
133 | if (pos >= L) return 0;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:134:35: error: ‘pos’ was not declared in this scope; did you mean ‘pow’?
134 | TSize ret = ordValue(text[pos]);
| ^~~
| pow
/<<PKGBUILDDIR>>/src/radix_inplace.h:134:21: error: there are no arguments to ‘ordValue’ that depend on a template parameter, so a declaration of ‘ordValue’ must be available [-fpermissive]
134 | TSize ret = ordValue(text[pos]);
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: At global scope:
/<<PKGBUILDDIR>>/src/radix_inplace.h:144:36: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
144 | struct RadixTextAccessor<TSAValue, StringSet<TString, TSetSpec>, void, TSize> :
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:144:63: error: template argument 2 is invalid
144 | struct RadixTextAccessor<TSAValue, StringSet<TString, TSetSpec>, void, TSize> :
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:175:53: error: ‘Nothing’ does not name a type
175 | template <typename TSAValue, typename TLimitsString=Nothing const>
| ^~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:175:61: error: expected ‘>’ before ‘const’
175 | template <typename TSAValue, typename TLimitsString=Nothing const>
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: In member function ‘bool seqan::_ZeroBucketComparator<TSAValue, TLimitsString>::operator()(const TSAValue&, const TSAValue&) const’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:183:18: error: expected nested-name-specifier before ‘Size’
183 | typename Size<TLimitsString>::Type lena = limits[getSeqNo(a)+1]-limits[getSeqNo(a)] - getSeqOffset(a);
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:183:18: error: expected ‘(’ before ‘Size’
/<<PKGBUILDDIR>>/src/radix_inplace.h:184:18: error: expected nested-name-specifier before ‘Size’
184 | typename Size<TLimitsString>::Type lenb = limits[getSeqNo(b)+1]-limits[getSeqNo(b)] - getSeqOffset(b);
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:184:18: error: expected ‘(’ before ‘Size’
/<<PKGBUILDDIR>>/src/radix_inplace.h:185:13: error: ‘lena’ was not declared in this scope
185 | if (lena == lenb)
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:185:21: error: ‘lenb’ was not declared in this scope
185 | if (lena == lenb)
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: At global scope:
/<<PKGBUILDDIR>>/src/radix_inplace.h:197:40: error: ‘Nothing’ was not declared in this scope; did you mean ‘seqan2::Nothing’?
197 | struct _ZeroBucketComparator<TSAValue, Nothing const>
| ^~~~~~~
| seqan2::Nothing
In file included from /usr/include/seqan/basic/basic_fundamental.h:66,
from /usr/include/seqan/basic.h:58:
/usr/include/seqan/basic/fundamental_tags.h:131:23: note: ‘seqan2::Nothing’ declared here
131 | typedef Tag<Nothing_> Nothing;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:197:53: error: template argument 2 is invalid
197 | struct _ZeroBucketComparator<TSAValue, Nothing const>
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:219:22: error: expected nested-name-specifier before ‘StringSetLimits’
219 | typedef typename StringSetLimits<TText const>::Type TLimitsString; // "Nothing" for Strings
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:219:22: error: expected ‘;’ at end of member declaration
219 | typedef typename StringSetLimits<TText const>::Type TLimitsString; // "Nothing" for Strings
| ^~~~~~~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:219:37: error: expected unqualified-id before ‘<’ token
219 | typedef typename StringSetLimits<TText const>::Type TLimitsString; // "Nothing" for Strings
| ^
In file included from /<<PKGBUILDDIR>>/src/lambda.cpp:33:
/<<PKGBUILDDIR>>/src/holders.hpp: In function ‘void printStats(const StatsHolder&, const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/holders.hpp:141:24: error: ‘_numberOfDigits’ was not declared in this scope; did you mean ‘seqan2::_numberOfDigits’?
141 | auto const w = _numberOfDigits(rem); // number of digits
| ^~~~~~~~~~~~~~~
| seqan2::_numberOfDigits
In file included from /usr/include/seqan/blast.h:67:
/usr/include/seqan/blast/blast_report_out.h:192:1: note: ‘seqan2::_numberOfDigits’ declared here
192 | _numberOfDigits(T const number)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:221:45: error: ‘TLimitsString’ was not declared in this scope
221 | typedef _ZeroBucketComparator<TSAValue, TLimitsString> TOrderFunctor;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:221:58: error: template argument 2 is invalid
221 | typedef _ZeroBucketComparator<TSAValue, TLimitsString> TOrderFunctor;
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:182:24: error: ‘_numberOfDigits’ was not declared in this scope; did you mean ‘seqan2::_numberOfDigits’?
182 | auto const w = _numberOfDigits(stats.hitsFinal);
| ^~~~~~~~~~~~~~~
| seqan2::_numberOfDigits
/usr/include/seqan/blast/blast_report_out.h:192:1: note: ‘seqan2::_numberOfDigits’ declared here
192 | _numberOfDigits(T const number)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp: At global scope:
/<<PKGBUILDDIR>>/src/holders.hpp:215:11: error: ‘BlastProgram’ has not been declared
215 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:216:11: error: ‘BlastTabularSpec’ has not been declared
216 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: In function ‘void seqan::_radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> >&, RadixSortContext_<TSAValue, TText, TSize, Q>&, const std::tuple<TSAValue*, TSAValue*, TSize>&)’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:337:51: error: ‘SuffixLess_’ was not declared in this scope; did you mean ‘seqan2::SuffixLess_’?
337 | std::sort(std::get<0>(i), std::get<1>(i), SuffixLess_<TSAValue, TText const>(context.text, std::get<2>(i)));
| ^~~~~~~~~~~
| seqan2::SuffixLess_
In file included from /usr/include/seqan/index.h:102:
/usr/include/seqan/index/index_sa_qsort.h:45:12: note: ‘seqan2::SuffixLess_’ declared here
45 | struct SuffixLess_ :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:337:71: error: expected primary-expression before ‘,’ token
337 | std::sort(std::get<0>(i), std::get<1>(i), SuffixLess_<TSAValue, TText const>(context.text, std::get<2>(i)));
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:337:79: error: expected primary-expression before ‘const’
337 | std::sort(std::get<0>(i), std::get<1>(i), SuffixLess_<TSAValue, TText const>(context.text, std::get<2>(i)));
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: In function ‘void seqan::inPlaceRadixSort(TSA&, const TText&, const TLambda&)’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:363:22: error: expected nested-name-specifier before ‘Value’
363 | typedef typename Value<typename Concatenator<TText>::Type>::Type TAlphabet;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:363:27: error: expected initializer before ‘<’ token
363 | typedef typename Value<typename Concatenator<TText>::Type>::Type TAlphabet;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:364:22: error: expected nested-name-specifier before ‘Value’
364 | typedef typename Value<TSA>::Type TSAValue;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:364:27: error: expected initializer before ‘<’ token
364 | typedef typename Value<TSA>::Type TSAValue;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:365:22: error: expected nested-name-specifier before ‘Size’
365 | typedef typename Size<TText>::Type TSize;
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:365:26: error: expected initializer before ‘<’ token
365 | typedef typename Size<TText>::Type TSize;
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:220:28: error: ‘RedAlph’ does not name a type; did you mean ‘TRedAlph_’?
220 | using TRedAlph = RedAlph<p, TRedAlph_>; // ensures == Dna5 for BlastN
| ^~~~~~~
| TRedAlph_
/<<PKGBUILDDIR>>/src/radix_inplace.h:366:24: error: ‘TSAValue’ was not declared in this scope; did you mean ‘SAValue’?
366 | typedef std::tuple<TSAValue*, TSAValue*, TSize> TItem;
| ^~~~~~~~
| SAValue
/<<PKGBUILDDIR>>/src/radix_inplace.h:366:51: error: template argument 1 is invalid
366 | typedef std::tuple<TSAValue*, TSAValue*, TSize> TItem;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:366:51: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/src/radix_inplace.h:368:57: error: ‘ValueSize’ was not declared in this scope; did you mean ‘seqan2::ValueSize’?
368 | static const unsigned SIGMA = static_cast<unsigned>(ValueSize<TAlphabet>::VALUE) + 1;
| ^~~~~~~~~
| seqan2::ValueSize
In file included from /usr/include/seqan/basic/basic_fundamental.h:75:
/usr/include/seqan/basic/fundamental_comparison.h:47:30: note: ‘seqan2::ValueSize’ declared here
47 | template <typename T> struct ValueSize;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:221:34: error: ‘TRedAlph’ was not declared in this scope; did you mean ‘TRedAlph_’?
221 | using TMatch = Match<TRedAlph>;
| ^~~~~~~~
| TRedAlph_
/<<PKGBUILDDIR>>/src/holders.hpp:221:42: error: template argument 1 is invalid
221 | using TMatch = Match<TRedAlph>;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:368:67: error: ‘TAlphabet’ was not declared in this scope
368 | static const unsigned SIGMA = static_cast<unsigned>(ValueSize<TAlphabet>::VALUE) + 1;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:223:22: error: ‘BlastProgram’ does not name a type
223 | static constexpr BlastProgram blastProgram = p;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:368:79: error: ‘::VALUE’ has not been declared
368 | static const unsigned SIGMA = static_cast<unsigned>(ValueSize<TAlphabet>::VALUE) + 1;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:371:48: error: ‘TSize’ was not declared in this scope
371 | typedef RadixSortContext_<TSAValue, TText, TSize, SIGMA> TContext;
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:371:60: error: template argument 3 is invalid
371 | typedef RadixSortContext_<TSAValue, TText, TSize, SIGMA> TContext;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:371:60: error: the value of ‘SIGMA’ is not usable in a constant expression
/<<PKGBUILDDIR>>/src/radix_inplace.h:371:60: note: in template argument for type ‘unsigned int’
/<<PKGBUILDDIR>>/src/holders.hpp:224:77: error: ‘TFMIndex’ was not declared in this scope
224 | static constexpr bool indexIsFM = std::is_same<TIndexSpec_, TFMIndex<>>::value;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:224:85: error: template argument 2 is invalid
224 | static constexpr bool indexIsFM = std::is_same<TIndexSpec_, TFMIndex<>>::value;
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:224:90: error: ‘::value’ has not been declared; did you mean ‘seqan2::value’?
224 | static constexpr bool indexIsFM = std::is_same<TIndexSpec_, TFMIndex<>>::value;
| ^~~~~
| seqan2::value
In file included from /usr/include/seqan/seeds.h:76,
from /usr/include/seqan/align_extend.h:42,
from /<<PKGBUILDDIR>>/src/holders.hpp:25:
/usr/include/seqan/seeds/basic_iter_indirect.h:173:1: note: ‘seqan2::value’ declared here
173 | value(Iter<TContainer, Indirect<TWrappedIter> > const & iter)
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:392:22: error: no matching function for call to ‘_radixSortWrapper(std::vector<int>&, TContext&, TItem)’
392 | _radixSortWrapper(firstStack, firstSecondContext, TItem(&sa[0], &sa[0]+length(sa), 0));
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:332:1: note: candidate: ‘template<class TSAValue, class TSize, class TText, unsigned int Q> void seqan::_radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> >&, RadixSortContext_<TSAValue, TText, TSize, Q>&, const std::tuple<TSAValue*, TSAValue*, TSize>&)’
332 | _radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> > & stack,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:332:1: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:392:22: note: mismatched types ‘std::tuple<TSAValue*, TSAValue*, TSize>’ and ‘int’
392 | _radixSortWrapper(firstStack, firstSecondContext, TItem(&sa[0], &sa[0]+length(sa), 0));
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:401:34: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
401 | for (unsigned j = 0; j < length(firstStack); ++j)
| ^~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:402:30: error: no matching function for call to ‘_radixSortWrapper(__gnu_cxx::__alloc_traits<std::allocator<std::vector<int> >, std::vector<int> >::value_type&, __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type&, __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type&)’
402 | _radixSortWrapper(lStack[I_THREAD], lContext[I_THREAD], firstStack[j]);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:332:1: note: candidate: ‘template<class TSAValue, class TSize, class TText, unsigned int Q> void seqan::_radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> >&, RadixSortContext_<TSAValue, TText, TSize, Q>&, const std::tuple<TSAValue*, TSAValue*, TSize>&)’
332 | _radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> > & stack,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:332:1: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:402:30: note: mismatched types ‘std::tuple<TSAValue*, TSAValue*, TSize>’ and ‘int’
402 | _radixSortWrapper(lStack[I_THREAD], lContext[I_THREAD], firstStack[j]);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: In lambda function:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: no matching function for call to ‘get<1>(const TItem&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
from /usr/include/c++/14/string:51:
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’
1250 | get(pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’
1255 | get(pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’
1260 | get(const pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(const pair<_Tp1, _Tp2>&&)’
1265 | get(const pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
In file included from /usr/include/c++/14/bits/memory_resource.h:47,
from /usr/include/c++/14/string:68:
/usr/include/c++/14/tuple:2443:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(tuple<_Elements ...>&)’
2443 | get(tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2443:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2449:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(const tuple<_Elements ...>&)’
2449 | get(const tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2449:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2455:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(tuple<_Elements ...>&&)’
2455 | get(tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2455:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2464:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(const tuple<_Elements ...>&&)’
2464 | get(const tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2464:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
In file included from /usr/include/seqan/sequence.h:68:
/usr/include/c++/14/array:390:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp& std::get(array<_Tp, _Nm>&)’
390 | get(array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:390:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:399:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp&& std::get(array<_Tp, _Nm>&&)’
399 | get(array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:399:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:408:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp& std::get(const array<_Tp, _Nm>&)’
408 | get(const array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:408:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:417:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp&& std::get(const array<_Tp, _Nm>&&)’
417 | get(const array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:417:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
1272 | get(pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
1277 | get(const pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
1282 | get(pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
1287 | get(const pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
1292 | get(pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
1297 | get(const pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
1302 | get(pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
1307 | get(const pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2474:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__enable_if_t<(__i >= sizeof... (_Types))> std::get(const tuple<_Elements ...>&)’ (deleted)
2474 | get(const tuple<_Elements...>&) = delete;
| ^~~
/usr/include/c++/14/tuple:2474:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2481:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
2481 | get(tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2481:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2492:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
2492 | get(tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2492:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2503:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
2503 | get(const tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2503:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2515:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
2515 | get(const tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2515:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:37: note: expected a type, got ‘1’
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: no matching function for call to ‘get<0>(const TItem&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’
1250 | get(pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’
1255 | get(pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’
1260 | get(const pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(const pair<_Tp1, _Tp2>&&)’
1265 | get(const pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2443:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(tuple<_Elements ...>&)’
2443 | get(tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2443:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2449:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(const tuple<_Elements ...>&)’
2449 | get(const tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2449:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2455:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(tuple<_Elements ...>&&)’
2455 | get(tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2455:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2464:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(const tuple<_Elements ...>&&)’
2464 | get(const tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2464:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:390:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp& std::get(array<_Tp, _Nm>&)’
390 | get(array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:390:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:399:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp&& std::get(array<_Tp, _Nm>&&)’
399 | get(array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:399:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:408:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp& std::get(const array<_Tp, _Nm>&)’
408 | get(const array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:408:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:417:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp&& std::get(const array<_Tp, _Nm>&&)’
417 | get(const array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:417:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
1272 | get(pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
1277 | get(const pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
1282 | get(pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
1287 | get(const pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
1292 | get(pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
1297 | get(const pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
1302 | get(pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
1307 | get(const pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2474:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__enable_if_t<(__i >= sizeof... (_Types))> std::get(const tuple<_Elements ...>&)’ (deleted)
2474 | get(const tuple<_Elements...>&) = delete;
| ^~~
/usr/include/c++/14/tuple:2474:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2481:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
2481 | get(tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2481:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2492:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
2492 | get(tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2492:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2503:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
2503 | get(const tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2503:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2515:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
2515 | get(const tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2515:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:54: note: expected a type, got ‘0’
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: no matching function for call to ‘get<1>(const TItem&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’
1250 | get(pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’
1255 | get(pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’
1260 | get(const pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(const pair<_Tp1, _Tp2>&&)’
1265 | get(const pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2443:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(tuple<_Elements ...>&)’
2443 | get(tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2443:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2449:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(const tuple<_Elements ...>&)’
2449 | get(const tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2449:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2455:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(tuple<_Elements ...>&&)’
2455 | get(tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2455:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2464:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(const tuple<_Elements ...>&&)’
2464 | get(const tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2464:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:390:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp& std::get(array<_Tp, _Nm>&)’
390 | get(array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:390:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:399:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp&& std::get(array<_Tp, _Nm>&&)’
399 | get(array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:399:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:408:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp& std::get(const array<_Tp, _Nm>&)’
408 | get(const array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:408:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:417:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp&& std::get(const array<_Tp, _Nm>&&)’
417 | get(const array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:417:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
1272 | get(pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
1277 | get(const pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
1282 | get(pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
1287 | get(const pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
1292 | get(pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
1297 | get(const pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
1302 | get(pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
1307 | get(const pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2474:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__enable_if_t<(__i >= sizeof... (_Types))> std::get(const tuple<_Elements ...>&)’ (deleted)
2474 | get(const tuple<_Elements...>&) = delete;
| ^~~
/usr/include/c++/14/tuple:2474:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2481:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
2481 | get(tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2481:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2492:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
2492 | get(tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2492:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2503:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
2503 | get(const tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2503:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2515:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
2515 | get(const tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2515:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:73: note: expected a type, got ‘1’
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: no matching function for call to ‘get<0>(const TItem&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’
1250 | get(pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’
1255 | get(pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’
1260 | get(const pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(const pair<_Tp1, _Tp2>&&)’
1265 | get(const pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2443:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(tuple<_Elements ...>&)’
2443 | get(tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2443:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2449:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(const tuple<_Elements ...>&)’
2449 | get(const tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2449:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2455:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(tuple<_Elements ...>&&)’
2455 | get(tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2455:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2464:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(const tuple<_Elements ...>&&)’
2464 | get(const tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2464:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:390:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp& std::get(array<_Tp, _Nm>&)’
390 | get(array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:390:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:399:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp&& std::get(array<_Tp, _Nm>&&)’
399 | get(array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:399:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:408:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp& std::get(const array<_Tp, _Nm>&)’
408 | get(const array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:408:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/array:417:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp&& std::get(const array<_Tp, _Nm>&&)’
417 | get(const array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:417:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
1272 | get(pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
1277 | get(const pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
1282 | get(pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
1287 | get(const pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
1292 | get(pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
1297 | get(const pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
1302 | get(pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
1307 | get(const pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2474:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__enable_if_t<(__i >= sizeof... (_Types))> std::get(const tuple<_Elements ...>&)’ (deleted)
2474 | get(const tuple<_Elements...>&) = delete;
| ^~~
/usr/include/c++/14/tuple:2474:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘const TItem’ {aka ‘const int’}
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/usr/include/c++/14/tuple:2481:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
2481 | get(tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2481:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2492:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
2492 | get(tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2492:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2503:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
2503 | get(const tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2503:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2515:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
2515 | get(const tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2515:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
416 | return (std::get<1>(l) - std::get<0>(l)) > (std::get<1>(r) - std::get<0>(r));
| ~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:416:90: note: expected a type, got ‘0’
/<<PKGBUILDDIR>>/src/radix_inplace.h: In function ‘void seqan::inPlaceRadixSort(TSA&, const TText&, const TLambda&)’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: no matching function for call to ‘get<1>(__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’
1250 | get(pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’
1255 | get(pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’
1260 | get(const pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(const pair<_Tp1, _Tp2>&&)’
1265 | get(const pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2443:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(tuple<_Elements ...>&)’
2443 | get(tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2443:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2449:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(const tuple<_Elements ...>&)’
2449 | get(const tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2449:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2455:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(tuple<_Elements ...>&&)’
2455 | get(tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2455:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2464:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(const tuple<_Elements ...>&&)’
2464 | get(const tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2464:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:390:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp& std::get(array<_Tp, _Nm>&)’
390 | get(array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:390:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:399:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp&& std::get(array<_Tp, _Nm>&&)’
399 | get(array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:399:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:408:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp& std::get(const array<_Tp, _Nm>&)’
408 | get(const array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:408:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:417:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp&& std::get(const array<_Tp, _Nm>&&)’
417 | get(const array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:417:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
1272 | get(pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
1277 | get(const pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
1282 | get(pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
1287 | get(const pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
1292 | get(pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
1297 | get(const pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
1302 | get(pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
1307 | get(const pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2474:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__enable_if_t<(__i >= sizeof... (_Types))> std::get(const tuple<_Elements ...>&)’ (deleted)
2474 | get(const tuple<_Elements...>&) = delete;
| ^~~
/usr/include/c++/14/tuple:2474:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2481:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
2481 | get(tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2481:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2492:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
2492 | get(tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2492:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2503:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
2503 | get(const tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2503:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/usr/include/c++/14/tuple:2515:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
2515 | get(const tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2515:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:34: note: expected a type, got ‘1’
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: no matching function for call to ‘get<0>(__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’
1250 | get(pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1250:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’
1255 | get(pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1255:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’
1260 | get(const pair<_Tp1, _Tp2>& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1260:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: candidate: ‘template<long unsigned int _Int, class _Tp1, class _Tp2> constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(const pair<_Tp1, _Tp2>&&)’
1265 | get(const pair<_Tp1, _Tp2>&& __in) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1265:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::pair<_Tp1, _Tp2>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2443:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(tuple<_Elements ...>&)’
2443 | get(tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2443:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2449:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >& std::get(const tuple<_Elements ...>&)’
2449 | get(const tuple<_Elements...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2449:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2455:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(tuple<_Elements ...>&&)’
2455 | get(tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2455:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2464:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__tuple_element_t<__i, std::tuple<_Elements ...> >&& std::get(const tuple<_Elements ...>&&)’
2464 | get(const tuple<_Elements...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2464:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:390:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp& std::get(array<_Tp, _Nm>&)’
390 | get(array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:390:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:399:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr _Tp&& std::get(array<_Tp, _Nm>&&)’
399 | get(array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:399:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:408:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp& std::get(const array<_Tp, _Nm>&)’
408 | get(const array<_Tp, _Nm>& __arr) noexcept
| ^~~
/usr/include/c++/14/array:408:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/array:417:5: note: candidate: ‘template<long unsigned int _Int, class _Tp, long unsigned int _Nm> constexpr const _Tp&& std::get(const array<_Tp, _Nm>&&)’
417 | get(const array<_Tp, _Nm>&& __arr) noexcept
| ^~~
/usr/include/c++/14/array:417:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::array<_Tp, _Nm>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
1272 | get(pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1272:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_T1, _T2>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
1277 | get(const pair<_Tp, _Up>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1277:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_T1, _T2>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
1282 | get(pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1282:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_T1, _T2>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
1287 | get(const pair<_Tp, _Up>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1287:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_T1, _T2>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
1292 | get(pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1292:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp& std::get(pair<_Up, _Tp>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
1297 | get(const pair<_Up, _Tp>& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1297:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp& std::get(const pair<_Up, _Tp>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: candidate: ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
1302 | get(pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1302:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr _Tp&& std::get(pair<_Up, _Tp>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: candidate: ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
1307 | get(const pair<_Up, _Tp>&& __p) noexcept
| ^~~
/usr/include/c++/14/bits/stl_pair.h:1307:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Up> constexpr const _Tp&& std::get(const pair<_Up, _Tp>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2474:5: note: candidate: ‘template<long unsigned int __i, class ... _Elements> constexpr std::__enable_if_t<(__i >= sizeof... (_Types))> std::get(const tuple<_Elements ...>&)’ (deleted)
2474 | get(const tuple<_Elements...>&) = delete;
| ^~~
/usr/include/c++/14/tuple:2474:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: mismatched types ‘const std::tuple<_Elements ...>’ and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’}
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/tuple:2481:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
2481 | get(tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2481:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp& std::get(tuple<_Elements ...>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2492:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
2492 | get(tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2492:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr _Tp&& std::get(tuple<_Elements ...>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2503:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
2503 | get(const tuple<_Types...>& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2503:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp& std::get(const tuple<_Elements ...>&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/usr/include/c++/14/tuple:2515:5: note: candidate: ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
2515 | get(const tuple<_Types...>&& __t) noexcept
| ^~~
/usr/include/c++/14/tuple:2515:5: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class ... _Types> constexpr const _Tp&& std::get(const tuple<_Elements ...>&&)’
422 | if ((uint64_t(std::get<1>(secondStack.front()) - std::get<0>(secondStack.front())) <= (length(sa) / N_THREADS))
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:422:69: note: expected a type, got ‘0’
/<<PKGBUILDDIR>>/src/radix_inplace.h:443:30: error: no matching function for call to ‘_radixSortWrapper(__gnu_cxx::__alloc_traits<std::allocator<std::vector<int> >, std::vector<int> >::value_type&, __gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type&, TItem&)’
443 | _radixSortWrapper(lStack[I_THREAD], lContext[I_THREAD], i);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:332:1: note: candidate: ‘template<class TSAValue, class TSize, class TText, unsigned int Q> void seqan::_radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> >&, RadixSortContext_<TSAValue, TText, TSize, Q>&, const std::tuple<TSAValue*, TSAValue*, TSize>&)’
332 | _radixSortWrapper(std::vector<std::tuple<TSAValue*, TSAValue*, TSize> > & stack,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:332:1: note: template argument deduction/substitution failed:
/<<PKGBUILDDIR>>/src/radix_inplace.h:443:30: note: mismatched types ‘std::tuple<TSAValue*, TSAValue*, TSize>’ and ‘int’
443 | _radixSortWrapper(lStack[I_THREAD], lContext[I_THREAD], i);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: At global scope:
/<<PKGBUILDDIR>>/src/radix_inplace.h:464:19: error: ‘StringSet’ has not been declared
464 | StringSet<TString, TSSetSpec> const & s,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:464:28: error: expected ‘,’ or ‘...’ before ‘<’ token
464 | StringSet<TString, TSSetSpec> const & s,
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:225:65: error: ‘TransAlph’ was not declared in this scope
225 | static constexpr bool alphReduction = !std::is_same<TransAlph<p>, TRedAlph>::value;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: In function ‘void seqan::createSuffixArray(TSA&, int)’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:468:22: error: expected nested-name-specifier before ‘Size’
468 | typedef typename Size<TSA>::Type TSize;
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:468:26: error: expected initializer before ‘<’ token
468 | typedef typename Size<TSA>::Type TSize;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:469:22: error: expected nested-name-specifier before ‘Iterator’
469 | typedef typename Iterator<TSA, Standard>::Type TIter;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:469:30: error: expected initializer before ‘<’ token
469 | typedef typename Iterator<TSA, Standard>::Type TIter;
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:472:5: error: ‘TIter’ was not declared in this scope
472 | TIter it = begin(SA, Standard());
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:225:75: error: ‘p’ was not declared in this scope
225 | static constexpr bool alphReduction = !std::is_same<TransAlph<p>, TRedAlph>::value;
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:225:76: error: wrong number of template arguments (1, should be 2)
225 | static constexpr bool alphReduction = !std::is_same<TransAlph<p>, TRedAlph>::value;
| ^
/usr/include/c++/14/type_traits:780:12: note: provided for ‘template<class, class> struct std::is_same’
780 | struct is_same;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:225:79: error: ‘constexpr’ static data member ‘TRedAlph’ must have an initializer
225 | static constexpr bool alphReduction = !std::is_same<TransAlph<p>, TRedAlph>::value;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:225:79: error: expected ‘;’ at end of member declaration
225 | static constexpr bool alphReduction = !std::is_same<TransAlph<p>, TRedAlph>::value;
| ^~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/holders.hpp:225:87: error: expected unqualified-id before ‘>’ token
225 | static constexpr bool alphReduction = !std::is_same<TransAlph<p>, TRedAlph>::value;
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:228:27: error: ‘Alloc’ does not name a type; did you mean ‘alloca’?
228 | using TStringTag = Alloc<>;
| ^~~~~
| alloca
/<<PKGBUILDDIR>>/src/holders.hpp:230:30: error: ‘MMap’ does not name a type
230 | using TDirectStringTag = MMap<>;
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:473:36: error: ‘s’ was not declared in this scope
473 | for(unsigned j = 0; j < length(s); ++j)
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h:473:29: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
473 | for(unsigned j = 0; j < length(s); ++j)
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:234:22: error: ‘TStringTag’ does not name a type
234 | using TQryTag = TStringTag;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:475:9: error: ‘TSize’ was not declared in this scope
475 | TSize len = length(s[j]);
| ^~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:476:18: error: expected ‘;’ before ‘i’
476 | for(TSize i = 0; i < len; ++i, ++it)
| ^~
| ;
/<<PKGBUILDDIR>>/src/radix_inplace.h:476:26: error: ‘i’ was not declared in this scope
476 | for(TSize i = 0; i < len; ++i, ++it)
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:235:22: error: ‘TDirectStringTag’ does not name a type
235 | using TSubjTag = TDirectStringTag; // even if subjects were translated they are now loaded from disk
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:476:30: error: ‘len’ was not declared in this scope
476 | for(TSize i = 0; i < len; ++i, ++it)
| ^~~
/<<PKGBUILDDIR>>/src/holders.hpp:238:29: error: ‘StringSet’ does not name a type
238 | using TUntransQrySeqs = StringSet<String<OrigQryAlph<p>, TQryTag>, Owner<ConcatDirect<>>>;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:242:28: error: ‘StringSet’ does not name a type
242 | using TTransSeqs = StringSet<String<TransAlph<p>, TSpec>, Owner<ConcatDirect<>>>;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:476:42: error: ‘it’ was not declared in this scope; did you mean ‘int’?
476 | for(TSize i = 0; i < len; ++i, ++it)
| ^~
| int
/<<PKGBUILDDIR>>/src/radix_inplace.h:477:19: error: ‘Pair’ was not declared in this scope; did you mean ‘seqan2::Pair’?
477 | *it = Pair<unsigned, TSize>(j, i);
| ^~~~
| seqan2::Pair
In file included from /usr/include/seqan/basic/basic_metaprogramming.h:59,
from /usr/include/seqan/basic.h:52:
/usr/include/seqan/basic/metaprogramming_type_algebra.h:46:60: note: ‘seqan2::Pair’ declared here
46 | template <typename T1, typename T2, typename TSpec> struct Pair;
| ^~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:477:24: error: expected primary-expression before ‘unsigned’
477 | *it = Pair<unsigned, TSize>(j, i);
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:243:28: error: ‘TTransSeqs’ does not name a type
243 | using TTransQrySeqs = TTransSeqs<TQryTag>;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:481:26: error: ‘s’ was not declared in this scope
481 | inPlaceRadixSort(SA, s, progressCallback);
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:244:28: error: ‘TTransSeqs’ does not name a type
244 | using TTransSubjSeqs = TTransSeqs<TSubjTag>;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:481:29: error: ‘progressCallback’ was not declared in this scope
481 | inPlaceRadixSort(SA, s, progressCallback);
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h: At global scope:
/<<PKGBUILDDIR>>/src/radix_inplace.h:489:19: error: ‘StringSet’ has not been declared
489 | StringSet<TString, TSSetSpec> const & s,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/radix_inplace.h:489:28: error: expected ‘,’ or ‘...’ before ‘<’ token
489 | StringSet<TString, TSSetSpec> const & s,
| ^
/<<PKGBUILDDIR>>/src/radix_inplace.h: In function ‘void seqan::createSuffixArray(TSA&, int)’:
/<<PKGBUILDDIR>>/src/radix_inplace.h:492:27: error: ‘s’ was not declared in this scope
492 | createSuffixArray(SA, s, RadixSortSACreateTag(), [] (unsigned) {});
| ^
In file included from /<<PKGBUILDDIR>>/src/lambda_indexer.hpp:38:
/<<PKGBUILDDIR>>/src/lambda_indexer_misc.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer_misc.hpp:34:33: error: ‘Nothing’ was not declared in this scope; did you mean ‘seqan2::Nothing’?
34 | struct ComparisonCounter<TText, Nothing>
| ^~~~~~~
| seqan2::Nothing
/usr/include/seqan/basic/fundamental_tags.h:131:23: note: ‘seqan2::Nothing’ declared here
131 | typedef Tag<Nothing_> Nothing;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer_misc.hpp:34:40: error: template argument 2 is invalid
34 | struct ComparisonCounter<TText, Nothing>
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:247:29: error: ‘TTransSubjSeqs’ was not declared in this scope
247 | TTransSubjSeqs, // real type
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:48:20: error: ‘TCDStringSet’ was not declared in this scope
48 | loadSubjSeqsAndIds(TCDStringSet<String<TOrigAlph>> & originalSeqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:48:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
48 | loadSubjSeqsAndIds(TCDStringSet<String<TOrigAlph>> & originalSeqs,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:48:49: error: expected primary-expression before ‘>>’ token
48 | loadSubjSeqsAndIds(TCDStringSet<String<TOrigAlph>> & originalSeqs,
| ^~
/<<PKGBUILDDIR>>/src/holders.hpp:248:29: error: ‘TTransSubjSeqs’ was not declared in this scope
248 | TTransSubjSeqs &>::type; // will be initialized in constructor
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:248:45: error: template argument 2 is invalid
248 | TTransSubjSeqs &>::type; // will be initialized in constructor
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:248:45: error: template argument 3 is invalid
/<<PKGBUILDDIR>>/src/holders.hpp:248:46: error: expected identifier before ‘::’ token
248 | TTransSubjSeqs &>::type; // will be initialized in constructor
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:48:54: error: ‘originalSeqs’ was not declared in this scope
48 | loadSubjSeqsAndIds(TCDStringSet<String<TOrigAlph>> & originalSeqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:49:41: error: expected primary-expression before ‘const’
49 | LambdaIndexerOptions const & options)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:49:56: error: expression list treated as compound expression in initializer [-fpermissive]
49 | LambdaIndexerOptions const & options)
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:49:57: error: expected ‘;’ before ‘{’ token
49 | LambdaIndexerOptions const & options)
| ^
| ;
50 | {
| ~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp: In function ‘void _saveOriginalSeqLengths(TLimits, const LambdaIndexerOptions&)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:142:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’?
142 | CharString _path = options.dbFile;
| ^~~~~~~~~~
| seqan2::CharString
In file included from /usr/include/seqan/sequence.h:112:
/usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here
55 | typedef String<char, Alloc<void> > CharString;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:252:31: error: ‘ModifiedString’ does not name a type
252 | using TRedAlphModString = ModifiedString<String<TransAlph<p>, TSpec>,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:143:12: error: ‘_path’ was not declared in this scope
143 | append(_path, ".untranslengths");
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:143:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
143 | append(_path, ".untranslengths");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:144:18: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
144 | save(limits, toCString(_path));
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:153:1: error: variable or field ‘translateOrSwap’ declared void
153 | translateOrSwap(TCDStringSet<String<TTransAlph>> & out,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:257:29: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
257 | StringSet<TRedAlphModString<TQryTag>, Owner<ConcatDirect<>>>, // modview
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:153:17: error: ‘TCDStringSet’ was not declared in this scope
153 | translateOrSwap(TCDStringSet<String<TTransAlph>> & out,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:153:30: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
153 | translateOrSwap(TCDStringSet<String<TTransAlph>> & out,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:153:47: error: expected primary-expression before ‘>>’ token
153 | translateOrSwap(TCDStringSet<String<TTransAlph>> & out,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:153:52: error: ‘out’ was not declared in this scope
153 | translateOrSwap(TCDStringSet<String<TTransAlph>> & out,
| ^~~
/<<PKGBUILDDIR>>/src/holders.hpp:257:39: error: ‘TRedAlphModString’ was not declared in this scope
257 | StringSet<TRedAlphModString<TQryTag>, Owner<ConcatDirect<>>>, // modview
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:154:17: error: ‘TCDStringSet’ was not declared in this scope
154 | TCDStringSet<String<TOrigAlph>> & in,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:154:30: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
154 | TCDStringSet<String<TOrigAlph>> & in,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:154:46: error: expected primary-expression before ‘>>’ token
154 | TCDStringSet<String<TOrigAlph>> & in,
| ^~
/<<PKGBUILDDIR>>/src/holders.hpp:257:57: error: ‘TQryTag’ was not declared in this scope
257 | StringSet<TRedAlphModString<TQryTag>, Owner<ConcatDirect<>>>, // modview
| ^~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:257:64: error: wrong number of template arguments (2, should be 3)
257 | StringSet<TRedAlphModString<TQryTag>, Owner<ConcatDirect<>>>, // modview
| ^
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:257:65: error: expected identifier before ‘,’ token
257 | StringSet<TRedAlphModString<TQryTag>, Owner<ConcatDirect<>>>, // modview
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:154:51: error: ‘in’ was not declared in this scope; did you mean ‘seqan2::in’?
154 | TCDStringSet<String<TOrigAlph>> & in,
| ^~
| seqan2::in
In file included from /usr/include/seqan/index.h:47:
/usr/include/seqan/misc/set.h:268:5: note: ‘seqan2::in’ declared here
268 | in(TKey const &key, VectorSet_<TValue, TSpec> const &set) {
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:155:38: error: expected primary-expression before ‘const’
155 | LambdaIndexerOptions const & options)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:167:1: error: variable or field ‘translateOrSwap’ declared void
167 | translateOrSwap(TCDStringSet<String<TSameAlph>> & out,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:261:29: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
261 | StringSet<TRedAlphModString<TSubjTag>, Owner<ConcatDirect<>>>, // modview
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:167:17: error: ‘TCDStringSet’ was not declared in this scope
167 | translateOrSwap(TCDStringSet<String<TSameAlph>> & out,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:167:30: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
167 | translateOrSwap(TCDStringSet<String<TSameAlph>> & out,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:167:46: error: expected primary-expression before ‘>>’ token
167 | translateOrSwap(TCDStringSet<String<TSameAlph>> & out,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:167:51: error: ‘out’ was not declared in this scope
167 | translateOrSwap(TCDStringSet<String<TSameAlph>> & out,
| ^~~
/<<PKGBUILDDIR>>/src/holders.hpp:261:39: error: ‘TRedAlphModString’ was not declared in this scope
261 | StringSet<TRedAlphModString<TSubjTag>, Owner<ConcatDirect<>>>, // modview
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:168:17: error: ‘TCDStringSet’ was not declared in this scope
168 | TCDStringSet<String<TSameAlph>> & in,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:168:30: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
168 | TCDStringSet<String<TSameAlph>> & in,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:168:46: error: expected primary-expression before ‘>>’ token
168 | TCDStringSet<String<TSameAlph>> & in,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:168:51: error: ‘in’ was not declared in this scope; did you mean ‘seqan2::in’?
168 | TCDStringSet<String<TSameAlph>> & in,
| ^~
| seqan2::in
/usr/include/seqan/misc/set.h:268:5: note: ‘seqan2::in’ declared here
268 | in(TKey const &key, VectorSet_<TValue, TSpec> const &set) {
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:169:38: error: expected primary-expression before ‘const’
169 | LambdaIndexerOptions const & /**/)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:180:1: error: variable or field ‘dumpTranslatedSeqs’ declared void
180 | dumpTranslatedSeqs(TCDStringSet<String<TTransAlph>> const & translatedSeqs,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:261:57: error: ‘TSubjTag’ was not declared in this scope
261 | StringSet<TRedAlphModString<TSubjTag>, Owner<ConcatDirect<>>>, // modview
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:261:65: error: wrong number of template arguments (2, should be 3)
261 | StringSet<TRedAlphModString<TSubjTag>, Owner<ConcatDirect<>>>, // modview
| ^
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:261:66: error: expected identifier before ‘,’ token
261 | StringSet<TRedAlphModString<TSubjTag>, Owner<ConcatDirect<>>>, // modview
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:266:27: error: ‘StringSet’ does not name a type
266 | using TIds = StringSet<String<char, TSpec>, Owner<ConcatDirect<>>>;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:267:27: error: ‘TIds’ does not name a type
267 | using TQryIds = TIds<TQryTag>;
| ^~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:180:20: error: ‘TCDStringSet’ was not declared in this scope
180 | dumpTranslatedSeqs(TCDStringSet<String<TTransAlph>> const & translatedSeqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:268:27: error: ‘TIds’ does not name a type
268 | using TSubjIds = TIds<TSubjTag>;
| ^~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:180:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
180 | dumpTranslatedSeqs(TCDStringSet<String<TTransAlph>> const & translatedSeqs,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:180:50: error: expected primary-expression before ‘>>’ token
180 | dumpTranslatedSeqs(TCDStringSet<String<TTransAlph>> const & translatedSeqs,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:180:53: error: expected primary-expression before ‘const’
180 | dumpTranslatedSeqs(TCDStringSet<String<TTransAlph>> const & translatedSeqs,
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:181:41: error: expected primary-expression before ‘const’
181 | LambdaIndexerOptions const & options)
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:272:27: error: ‘Index’ does not name a type
272 | using TDbIndex = Index<typename std::remove_reference<TRedSubjSeqs>::type, TIndexSpec>;
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:275:69: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
275 | using TScoreScheme = std::conditional_t<std::is_same<TRedAlph, Dna5>::value,
| ^~~~
| seqan2::Dna5
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/holders.hpp:275:73: error: type/value mismatch at argument 1 in template parameter list for ‘template<class, class> struct std::is_same’
275 | using TScoreScheme = std::conditional_t<std::is_same<TRedAlph, Dna5>::value,
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:275:73: note: expected a type, got ‘GlobalDataHolder<TRedAlph_, TIndexSpec_, TFileFormat, <declaration error>, <declaration error> >::TRedAlph’
/<<PKGBUILDDIR>>/src/holders.hpp:275:73: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/src/holders.hpp:276:46: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
276 | Score<int, Simple>,
| ^~~~~
| seqan2::Score
In file included from /usr/include/seqan/score.h:45,
from /usr/include/seqan/graph_align.h:45,
from /usr/include/seqan/align.h:59,
from /usr/include/seqan/bam_io.h:50:
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:276:63: error: wrong number of template arguments (2, should be 3)
276 | Score<int, Simple>,
| ^
/usr/include/c++/14/type_traits:2715:11: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> using std::conditional_t = typename std::conditional::type’
2715 | using conditional_t = typename conditional<_Cond, _Iftrue, _Iffalse>::type;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:225:16: error: ‘TCDStringSet’ was not declared in this scope
225 | checkIndexSize(TCDStringSet<String<TRedAlph>> const & seqs)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:225:29: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
225 | checkIndexSize(TCDStringSet<String<TRedAlph>> const & seqs)
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:225:44: error: expected primary-expression before ‘>>’ token
225 | checkIndexSize(TCDStringSet<String<TRedAlph>> const & seqs)
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:225:47: error: expected primary-expression before ‘const’
225 | checkIndexSize(TCDStringSet<String<TRedAlph>> const & seqs)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:225:60: error: expected ‘;’ before ‘{’ token
225 | checkIndexSize(TCDStringSet<String<TRedAlph>> const & seqs)
| ^
| ;
226 | {
| ~
/<<PKGBUILDDIR>>/src/holders.hpp:279:27: error: ‘BlastIOContext’ does not name a type
279 | using TIOContext = BlastIOContext<TScoreScheme, p, h>;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp: In function ‘int convertMaskingFile(uint64_t, const LambdaIndexerOptions&)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:264:5: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
264 | StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntStarts;
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:264:15: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
264 | StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntStarts;
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:264:22: error: expected primary-expression before ‘unsigned’
264 | StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntStarts;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:265:22: error: expected primary-expression before ‘unsigned’
265 | StringSet<String<unsigned>, Owner<ConcatDirect<>>> segIntEnds;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:273:21: error: ‘toCString’ was not declared in this scope; did you mean ‘seqan2::toCString’?
273 | stream.open(toCString(options.segFile));
| ^~~~~~~~~
| seqan2::toCString
In file included from /usr/include/seqan/sequence.h:125:
/usr/include/seqan/sequence/adapt_stl_container.h:1291:1: note: ‘seqan2::toCString’ declared here
1291 | toCString(std::basic_string<TChar, TTraits, TAlloc> const & me)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:280:49: error: ‘Input’ was not declared in this scope; did you mean ‘seqan2::Input’?
280 | auto reader = directionIterator(stream, Input());
| ^~~~~
| seqan2::Input
/usr/include/seqan/file/file_interface.h:165:21: note: ‘seqan2::Input’ declared here
165 | typedef Tag<Input_> Input;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:280:23: error: ‘directionIterator’ was not declared in this scope; did you mean ‘seqan2::directionIterator’?
280 | auto reader = directionIterator(stream, Input());
| ^~~~~~~~~~~~~~~~~
| seqan2::directionIterator
/usr/include/seqan/stream/formatted_file.h:494:1: note: ‘seqan2::directionIterator’ declared here
494 | directionIterator(FormattedFile<TFileFormat, TDirection, TSpec> & file, TDirection const &)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:285:26: error: expected primary-expression before ‘unsigned’
285 | StringSet<String<unsigned>> _segIntStarts;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:286:26: error: expected primary-expression before ‘unsigned’
286 | StringSet<String<unsigned>> _segIntEnds;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:280:27: error: ‘FormattedFile’ does not name a type
280 | using TFile = FormattedFile<TFileFormat, Output, TIOContext>;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:281:27: error: ‘FormattedFile’ does not name a type
281 | using TBamFile = FormattedFile<Bam, Output, BlastTabular>;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:284:36: error: expected nested-name-specifier before ‘StringSetLimits’
284 | using TPositions = typename StringSetLimits<TTransQrySeqs>::Type;
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:285:27: error: ‘StringSet’ does not name a type
285 | using TMasking = StringSet<String<unsigned>, Owner<ConcatDirect<>>>;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:287:16: error: ‘_segIntStarts’ was not declared in this scope
287 | resize(_segIntStarts, numberOfSeqs, Exact());
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:287:45: error: ‘Exact’ was not declared in this scope; did you mean ‘seqan2::Exact’?
287 | resize(_segIntStarts, numberOfSeqs, Exact());
| ^~~~~
| seqan2::Exact
In file included from /usr/include/seqan/sequence.h:94:
/usr/include/seqan/sequence/sequence_interface.h:120:24: note: ‘seqan2::Exact’ declared here
120 | typedef Tag<TagExact_> Exact;
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:288:5: error: ‘TDbIndex’ does not name a type
288 | TDbIndex dbIndex;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:287:9: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
287 | resize(_segIntStarts, numberOfSeqs, Exact());
| ^~~~~~
| seqan2::resize
In file included from /usr/include/seqan/index.h:169:
/usr/include/seqan/index/index_fm_compressed_sa.h:456:1: note: ‘seqan2::resize’ declared here
456 | resize(CompressedSA<TText, TSpec, TConfig> & compressedSA, TSize size, Tag<TExpand> tag)
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:290:5: error: ‘TUntransQrySeqs’ does not name a type
290 | TUntransQrySeqs untranslatedQrySeqs; // used iff outformat is sam or bam
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:288:16: error: ‘_segIntEnds’ was not declared in this scope
288 | resize(_segIntEnds, numberOfSeqs, Exact());
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:289:9: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’?
289 | CharString buf;
| ^~~~~~~~~~
| seqan2::CharString
/usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here
55 | typedef String<char, Alloc<void> > CharString;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:292:5: error: ‘TTransQrySeqs’ does not name a type
292 | TTransQrySeqs qrySeqs;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:294:16: error: ‘value’ was not declared in this scope; did you mean ‘seqan2::value’?
294 | while (value(reader) == '>')
| ^~~~~
| seqan2::value
In file included from /usr/include/seqan/index.h:186:
/usr/include/seqan/index/index_esa_algs_multi.h:697:5: note: ‘seqan2::value’ declared here
697 | value(Iter<TRepeat, MultiMemOccurrences> &it) {
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:303:13: error: ‘skipLine’ was not declared in this scope; did you mean ‘seqan2::skipLine’?
303 | skipLine(reader);
| ^~~~~~~~
| seqan2::skipLine
In file included from /usr/include/seqan/stream.h:118:
/usr/include/seqan/stream/tokenization.h:457:13: note: ‘seqan2::skipLine’ declared here
457 | inline void skipLine(TFwdIterator &iter)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:304:17: error: ‘atEnd’ was not declared in this scope; did you mean ‘seqan2::atEnd’?
304 | if (atEnd(reader))
| ^~~~~
| seqan2::atEnd
In file included from /usr/include/seqan/blast.h:65:
/usr/include/seqan/blast/blast_tabular_in.h:155:1: note: ‘seqan2::atEnd’ declared here
155 | atEnd(BlastTabularFileIn<TContext> & formattedFile)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:308:22: error: ‘atEnd’ was not declared in this scope; did you mean ‘seqan2::atEnd’?
308 | while ((!atEnd(reader)) && (value(reader) != '>'))
| ^~~~~
| seqan2::atEnd
/usr/include/seqan/blast/blast_tabular_in.h:155:1: note: ‘seqan2::atEnd’ declared here
155 | atEnd(BlastTabularFileIn<TContext> & formattedFile)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:310:47: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
310 | resize(_segIntStarts[curSeq], length(_segIntStarts[curSeq])+1);
| ^~~~~~
| seqan2::length
In file included from /usr/include/seqan/index/index_pizzachili.h:39,
from /usr/include/seqan/index.h:194:
/usr/include/seqan/index/index_pizzachili_string.h:376:1: note: ‘seqan2::length’ declared here
376 | length(String<TValue, PizzaChili<TSpec> > const& me) {
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:293:5: error: ‘TTransSubjReal’ does not name a type
293 | TTransSubjReal subjSeqs;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:312:23: error: ‘buf’ was not declared in this scope
312 | clear(buf);
| ^~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:313:40: error: ‘IsWhitespace’ was not declared in this scope; did you mean ‘seqan2::IsWhitespace’?
313 | readUntil(buf, reader, IsWhitespace());
| ^~~~~~~~~~~~
| seqan2::IsWhitespace
/usr/include/seqan/stream/tokenization.h:149:65: note: ‘seqan2::IsWhitespace’ declared here
149 | typedef OrFunctor<IsBlank, IsNewline> IsWhitespace;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:313:17: error: ‘readUntil’ was not declared in this scope; did you mean ‘seqan2::readUntil’?
313 | readUntil(buf, reader, IsWhitespace());
| ^~~~~~~~~
| seqan2::readUntil
/usr/include/seqan/stream/tokenization.h:354:13: note: ‘seqan2::readUntil’ declared here
354 | inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:295:5: error: ‘TRedQrySeqs’ does not name a type
295 | TRedQrySeqs redQrySeqs;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:317:35: error: ‘IsDigit’ was not declared in this scope; did you mean ‘seqan2::IsDigit’?
317 | skipUntil(reader, IsDigit());
| ^~~~~~~
| seqan2::IsDigit
/usr/include/seqan/stream/tokenization.h:152:65: note: ‘seqan2::IsDigit’ declared here
152 | typedef IsInRange<'0', '9'> IsDigit;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:317:17: error: ‘skipUntil’ was not declared in this scope; did you mean ‘seqan2::skipUntil’?
317 | skipUntil(reader, IsDigit());
| ^~~~~~~~~
| seqan2::skipUntil
/usr/include/seqan/stream/tokenization.h:212:13: note: ‘seqan2::skipUntil’ declared here
212 | inline void skipUntil(TFwdIterator &iter, TStopFunctor const &stopFunctor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:330:17: error: ‘atEnd’ was not declared in this scope; did you mean ‘seqan2::atEnd’?
330 | if (atEnd(reader))
| ^~~~~
| seqan2::atEnd
/usr/include/seqan/blast/blast_tabular_in.h:155:1: note: ‘seqan2::atEnd’ declared here
155 | atEnd(BlastTabularFileIn<TContext> & formattedFile)
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:296:5: error: ‘TRedSubjSeqs’ does not name a type
296 | TRedSubjSeqs redSubjSeqs;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:298:5: error: ‘TQryIds’ does not name a type
298 | TQryIds qryIds;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:299:5: error: ‘TSubjIds’ does not name a type
299 | TSubjIds subjIds;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:344:9: error: ‘segIntStarts’ was not declared in this scope
344 | segIntStarts.concat = concat(_segIntStarts);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:344:31: error: ‘concat’ was not declared in this scope; did you mean ‘seqan2::concat’?
344 | segIntStarts.concat = concat(_segIntStarts);
| ^~~~~~
| seqan2::concat
In file included from /usr/include/seqan/sequence.h:136:
/usr/include/seqan/sequence/string_set_concat_direct.h:681:1: note: ‘seqan2::concat’ declared here
681 | concat(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me)
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:301:5: error: ‘TFile’ does not name a type; did you mean ‘gzFile’?
301 | TFile outfile;
| ^~~~~
| gzFile
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:345:31: error: ‘stringSetLimits’ was not declared in this scope; did you mean ‘seqan2::stringSetLimits’?
345 | segIntStarts.limits = stringSetLimits(_segIntStarts);
| ^~~~~~~~~~~~~~~
| seqan2::stringSetLimits
/usr/include/seqan/index/index_base.h:1395:5: note: ‘seqan2::stringSetLimits’ declared here
1395 | stringSetLimits(Index<StringSet<TString, TSSetSpec> const, TSpec> const &index) {
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:302:5: error: ‘TBamFile’ does not name a type
302 | TBamFile outfileBam;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:304:5: error: ‘TPositions’ does not name a type
304 | TPositions untransQrySeqLengths; // used iff qIsTranslated(p)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:346:9: error: ‘segIntEnds’ was not declared in this scope
346 | segIntEnds.concat = concat(_segIntEnds);
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:305:5: error: ‘TPositions’ does not name a type
305 | TPositions untransSubjSeqLengths; // used iff sIsTranslated(p)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:307:5: error: ‘TMasking’ does not name a type
307 | TMasking segIntStarts;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:357:16: error: ‘segIntStarts’ was not declared in this scope
357 | resize(segIntStarts, numberOfSeqs, Exact());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:357:44: error: ‘Exact’ was not declared in this scope; did you mean ‘seqan2::Exact’?
357 | resize(segIntStarts, numberOfSeqs, Exact());
| ^~~~~
| seqan2::Exact
/usr/include/seqan/sequence/sequence_interface.h:120:24: note: ‘seqan2::Exact’ declared here
120 | typedef Tag<TagExact_> Exact;
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:308:5: error: ‘TMasking’ does not name a type
308 | TMasking segIntEnds;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:357:36: error: expected nested-name-specifier before ‘Value’
357 | using TRedQrySeq = typename Value<typename std::remove_reference<typename TGlobalHolder::TRedQrySeqs>::type>::Type;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:357:9: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
357 | resize(segIntStarts, numberOfSeqs, Exact());
| ^~~~~~
| seqan2::resize
/usr/include/seqan/index/index_fm_compressed_sa.h:456:1: note: ‘seqan2::resize’ declared here
456 | resize(CompressedSA<TText, TSpec, TConfig> & compressedSA, TSize size, Tag<TExpand> tag)
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:358:27: error: ‘StringSet’ does not name a type
358 | using TSeeds = StringSet<typename Infix<TRedQrySeq const>::Type>;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:359:27: error: ‘Index’ does not name a type
359 | using TSeedIndex = Index<TSeeds, IndexSa<>>;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:358:16: error: ‘segIntEnds’ was not declared in this scope
358 | resize(segIntEnds, numberOfSeqs, Exact());
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:371:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’?
371 | CharString _path = options.dbFile;
| ^~~~~~~~~~
| seqan2::CharString
/usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here
55 | typedef String<char, Alloc<void> > CharString;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:366:22: error: ‘BlastProgram’ does not name a type
366 | static constexpr BlastProgram blastProgram = TGlobalHolder::blastProgram;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:376:5: error: ‘TSeeds’ does not name a type
376 | TSeeds seeds;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:372:12: error: ‘_path’ was not declared in this scope
372 | append(_path, ".binseg_s");
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:372:5: error: ‘append’ was not declared in this scope; did you mean ‘seqan2::append’?
372 | append(_path, ".binseg_s");
| ^~~~~~
| seqan2::append
In file included from /usr/include/seqan/pipe.h:73,
from /usr/include/seqan/index.h:42:
/usr/include/seqan/pipe/pool_base.h:1341:17: note: ‘seqan2::append’ declared here
1341 | inline bool append(Pool<TValue, TSpec> &dest, String<TValue, TStringSpec> &src) {
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:377:5: error: ‘TSeedIndex’ does not name a type
377 | TSeedIndex seedIndex;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:384:24: error: ‘Gaps’ does not name a type
384 | using TAlignRow0 = Gaps<typename Infix<typename Value<typename TGlobalHolder::TTransQrySeqs>::Type>::Type,
| ^~~~
/<<PKGBUILDDIR>>/src/holders.hpp:386:24: error: ‘Gaps’ does not name a type
386 | using TAlignRow1 = Gaps<typename Infix<typename Value<typename TGlobalHolder::TTransSubjSeqs>::Type>::Type,
| ^~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:373:10: error: ‘segIntStarts’ was not declared in this scope
373 | save(segIntStarts, toCString(_path));
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:392:25: error: ‘DPCell_’ does not name a type
392 | using TDPCell = DPCell_<TCellValue, TScoreExtension>;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:393:34: error: expected nested-name-specifier before ‘TraceBitMap_’
393 | using TTraceValue = typename TraceBitMap_<TCellValue>::Type;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:373:24: error: ‘toCString’ was not declared in this scope; did you mean ‘seqan2::toCString’?
373 | save(segIntStarts, toCString(_path));
| ^~~~~~~~~
| seqan2::toCString
/usr/include/seqan/sequence/adapt_stl_container.h:1291:1: note: ‘seqan2::toCString’ declared here
1291 | toCString(std::basic_string<TChar, TTraits, TAlloc> const & me)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:373:5: error: ‘save’ was not declared in this scope; did you mean ‘seqan2::save’?
373 | save(segIntStarts, toCString(_path));
| ^~~~
| seqan2::save
/usr/include/seqan/index/index_pizzachili.h:374:13: note: ‘seqan2::save’ declared here
374 | inline bool save(
| ^~~~
/<<PKGBUILDDIR>>/src/holders.hpp:394:25: error: ‘String’ does not name a type
394 | using TScoreHost = String<TDPCell, Alloc<OverAligned> >;
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:395:25: error: ‘String’ does not name a type
395 | using TTraceHost = String<TTraceValue, Alloc<OverAligned> >;
| ^~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:396:25: error: ‘DPContext’ does not name a type
396 | using TDPContext = DPContext<TDPCell, TTraceValue, TScoreHost, TTraceHost>;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:376:10: error: ‘segIntEnds’ was not declared in this scope
376 | save(segIntEnds, toCString(_path));
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:394:19: error: ‘StringSet’ has not been declared
394 | StringSet<TString, TSSetSpec> const & s,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:394:28: error: expected ‘,’ or ‘...’ before ‘<’ token
394 | StringSet<TString, TSSetSpec> const & s,
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:398:28: error: ‘AliExtContext_’ does not name a type
398 | using TAliExtContext = AliExtContext_<TAlignRow0, TAlignRow1, TDPContext>;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp: In function ‘void createSuffixArray(TSA&, int)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:398:34: error: ‘s’ was not declared in this scope
398 | return createSuffixArray(SA, s, TAlgo());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:21: error: ‘Index’ was not declared in this scope; did you mean ‘seqan2::Index’?
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^~~~~
| seqan2::Index
/usr/include/seqan/index/index_base.h:228:11: note: ‘seqan2::Index’ declared here
228 | class Index;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:32: error: expected primary-expression before ‘,’ token
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:34: error: ‘FMIndex’ was not declared in this scope; did you mean ‘seqan2::FMIndex’?
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^~~~~~~
| seqan2::FMIndex
/usr/include/seqan/index/index_fm.h:143:7: note: ‘seqan2::FMIndex’ declared here
143 | class FMIndex;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:47: error: expected primary-expression before ‘,’ token
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:56: error: expected primary-expression before ‘>’ token
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:58: error: expected primary-expression before ‘>’ token
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:408:21: error: ‘FibreSALF’ was not declared in this scope; did you mean ‘seqan2::FibreSALF’?
408 | FibreSALF const &,
| ^~~~~~~~~
| seqan2::FibreSALF
/usr/include/seqan/index/index_fm.h:156:41: note: ‘seqan2::FibreSALF’ declared here
156 | typedef Tag<FibreSALF_> const FibreSALF;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:409:29: error: expected primary-expression before ‘const’
409 | TLambda const & progressCallback)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:409:53: error: expression list treated as compound expression in initializer [-fpermissive]
409 | TLambda const & progressCallback)
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:409:54: error: expected ‘;’ before ‘{’ token
409 | TLambda const & progressCallback)
| ^
| ;
410 | {
| ~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:445:21: error: redeclaration of ‘template<class TText, class TSpec, class TLambda> bool indexCreateProgress’
445 | indexCreateProgress(Index<TText, IndexSa<TSpec> > & index,
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:407:1: note: previous declaration ‘template<class TText, class TSpec, class TConfig, class TLambda> bool indexCreateProgress<TText, TSpec, TConfig, TLambda>’
407 | indexCreateProgress(Index<TText, FMIndex<TSpec, TConfig> > & index,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:445:21: error: ‘Index’ was not declared in this scope; did you mean ‘seqan2::Index’?
445 | indexCreateProgress(Index<TText, IndexSa<TSpec> > & index,
| ^~~~~
| seqan2::Index
/usr/include/seqan/index/index_base.h:228:11: note: ‘seqan2::Index’ declared here
228 | class Index;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:445:32: error: expected primary-expression before ‘,’ token
445 | indexCreateProgress(Index<TText, IndexSa<TSpec> > & index,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:445:34: error: ‘IndexSa’ was not declared in this scope; did you mean ‘seqan2::IndexSa’?
445 | indexCreateProgress(Index<TText, IndexSa<TSpec> > & index,
| ^~~~~~~
| seqan2::IndexSa
/usr/include/seqan/index/index_sa_stree.h:58:8: note: ‘seqan2::IndexSa’ declared here
58 | struct IndexSa {};
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:445:47: error: expected primary-expression before ‘>’ token
445 | indexCreateProgress(Index<TText, IndexSa<TSpec> > & index,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:445:49: error: expected primary-expression before ‘>’ token
445 | indexCreateProgress(Index<TText, IndexSa<TSpec> > & index,
| ^
/<<PKGBUILDDIR>>/src/holders.hpp:400:5: error: ‘TAliExtContext’ does not name a type
400 | TAliExtContext alignContext;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:446:21: error: ‘FibreSA’ was not declared in this scope; did you mean ‘seqan2::FibreSA’?
446 | FibreSA const &,
| ^~~~~~~
| seqan2::FibreSA
/usr/include/seqan/index/index_base.h:458:40: note: ‘seqan2::FibreSA’ declared here
458 | typedef Tag<FibreSA_> const FibreSA;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:447:29: error: expected primary-expression before ‘const’
447 | TLambda const & progressCallback)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:447:53: error: expression list treated as compound expression in initializer [-fpermissive]
447 | TLambda const & progressCallback)
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:447:54: error: expected ‘;’ before ‘{’ token
447 | TLambda const & progressCallback)
| ^
| ;
448 | {
| ~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:484:11: error: ‘BlastProgram’ has not been declared
484 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:486:1: error: variable or field ‘generateIndexAndDump’ declared void
486 | generateIndexAndDump(StringSet<TString, TSpec> & seqs,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:486:22: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’?
486 | generateIndexAndDump(StringSet<TString, TSpec> & seqs,
| ^~~~~~~~~
| seqan2::StringSet
/usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here
50 | class StringSet;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:486:39: error: expected primary-expression before ‘,’ token
486 | generateIndexAndDump(StringSet<TString, TSpec> & seqs,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:486:46: error: expected primary-expression before ‘>’ token
486 | generateIndexAndDump(StringSet<TString, TSpec> & seqs,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:486:57: error: ‘seqs’ was not declared in this scope
486 | generateIndexAndDump(StringSet<TString, TSpec> & seqs,
| ^~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:487:49: error: expected primary-expression before ‘const’
487 | LambdaIndexerOptions const & options,
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:488:22: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
488 | BlastProgramSelector<p> const &,
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:488:43: error: ‘p’ was not declared in this scope
488 | BlastProgramSelector<p> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:488:49: error: expected primary-expression before ‘const’
488 | BlastProgramSelector<p> const &,
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.hpp:489:49: error: expected primary-expression before ‘const’
489 | TRedAlph_ const &)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:42:11: error: ‘BlastProgram’ has not been declared
42 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:45:10: error: ‘BlastProgramSelector’ has not been declared
45 | BlastProgramSelector<p> const &);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:45:30: error: expected ‘,’ or ‘...’ before ‘<’ token
45 | BlastProgramSelector<p> const &);
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:47:11: error: ‘BlastProgram’ has not been declared
47 | template <BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:51:10: error: ‘BlastProgramSelector’ has not been declared
51 | BlastProgramSelector<p> const &,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:51:30: error: expected ‘,’ or ‘...’ before ‘<’ token
51 | BlastProgramSelector<p> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:54:11: error: ‘BlastProgram’ has not been declared
54 | template <BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:59:10: error: ‘BlastProgramSelector’ has not been declared
59 | BlastProgramSelector<p> const &,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:59:30: error: expected ‘,’ or ‘...’ before ‘<’ token
59 | BlastProgramSelector<p> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:75:12: error: ‘ArgumentParser’ is not a member of ‘seqan’; did you mean ‘seqan2::ArgumentParser’?
75 | seqan::ArgumentParser parser;
| ^~~~~~~~~~~~~~
/usr/include/seqan/arg_parse/argument_parser.h:152:7: note: ‘seqan2::ArgumentParser’ declared here
152 | class ArgumentParser
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:77:12: error: ‘seqan::ArgumentParser’ has not been declared
77 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp: In member function ‘void LocalDataHolder<TGlobalHolder_, TScoreExtension>::init(uint64_t)’:
/<<PKGBUILDDIR>>/src/holders.hpp:431:58: error: ‘blastProgram’ was not declared in this scope
431 | indexBeginQry -= (indexBeginQry % qNumFrames(blastProgram));
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:431:47: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-fpermissive]
431 | indexBeginQry -= (indexBeginQry % qNumFrames(blastProgram));
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:432:43: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-fpermissive]
432 | indexEndQry -= (indexEndQry % qNumFrames(blastProgram));
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:82:9: error: ‘res’ was not declared in this scope
82 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:82:23: error: ‘seqan::ArgumentParser’ has not been declared
82 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:83:30: error: ‘seqan::ArgumentParser’ has not been declared
83 | return res == seqan::ArgumentParser::PARSE_ERROR;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: In function ‘int argConv0(const LambdaIndexerOptions&)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:93:20: error: ‘const struct LambdaIndexerOptions’ has no member named ‘blastProgram’
93 | switch(options.blastProgram)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:95:14: error: ‘BlastProgram’ has not been declared
95 | case BlastProgram::BLASTN:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:96:38: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
96 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTN>());
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:96:59: error: ‘BlastProgram’ has not been declared
96 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTN>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:96:81: error: expected primary-expression before ‘)’ token
96 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTN>());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:97:14: error: ‘BlastProgram’ has not been declared
97 | case BlastProgram::BLASTP:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:98:59: error: ‘BlastProgram’ has not been declared
98 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTP>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:98:81: error: expected primary-expression before ‘)’ token
98 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTP>());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:99:14: error: ‘BlastProgram’ has not been declared
99 | case BlastProgram::BLASTX:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:100:59: error: ‘BlastProgram’ has not been declared
100 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTX>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:100:81: error: expected primary-expression before ‘)’ token
100 | return argConv1(options, BlastProgramSelector<BlastProgram::BLASTX>());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:101:14: error: ‘BlastProgram’ has not been declared
101 | case BlastProgram::TBLASTN:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:102:59: error: ‘BlastProgram’ has not been declared
102 | return argConv1(options, BlastProgramSelector<BlastProgram::TBLASTN>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:102:82: error: expected primary-expression before ‘)’ token
102 | return argConv1(options, BlastProgramSelector<BlastProgram::TBLASTN>());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:103:14: error: ‘BlastProgram’ has not been declared
103 | case BlastProgram::TBLASTX:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:104:59: error: ‘BlastProgram’ has not been declared
104 | return argConv1(options, BlastProgramSelector<BlastProgram::TBLASTX>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:104:82: error: expected primary-expression before ‘)’ token
104 | return argConv1(options, BlastProgramSelector<BlastProgram::TBLASTX>());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:112:11: error: ‘BlastProgram’ has not been declared
112 | template <BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:115:10: error: ‘BlastProgramSelector’ has not been declared
115 | BlastProgramSelector<p> const &)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:115:30: error: expected ‘,’ or ‘...’ before ‘<’ token
115 | BlastProgramSelector<p> const &)
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: In function ‘int argConv1(const LambdaIndexerOptions&, int)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:117:46: error: ‘p’ was not declared in this scope
117 | using TUnred = typename std::conditional<p == BlastProgram::BLASTN, Dna5, AminoAcid>::type;
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:117:51: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’?
117 | using TUnred = typename std::conditional<p == BlastProgram::BLASTN, Dna5, AminoAcid>::type;
| ^~~~~~~~~~~~
| seqan2::BlastProgram
/usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here
84 | enum class BlastProgram : uint8_t
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:117:88: error: wrong number of template arguments (1, should be 3)
117 | using TUnred = typename std::conditional<p == BlastProgram::BLASTN, Dna5, AminoAcid>::type;
| ^
/usr/include/c++/14/type_traits:2334:12: note: provided for ‘template<bool _Cond, class _Iftrue, class _Iffalse> struct std::conditional’
2334 | struct conditional
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:117:89: error: expected identifier before ‘::’ token
117 | using TUnred = typename std::conditional<p == BlastProgram::BLASTN, Dna5, AminoAcid>::type;
| ^~
/<<PKGBUILDDIR>>/src/holders.hpp:435:40: error: ‘blastProgram’ was not declared in this scope
435 | indexBeginQry = qNumFrames(blastProgram) * i;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:435:29: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-fpermissive]
435 | indexBeginQry = qNumFrames(blastProgram) * i;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:436:27: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-fpermissive]
436 | indexEndQry = qNumFrames(blastProgram) * (i+1);
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:118:16: error: ‘BlastProgramSelector’ does not name a type
118 | using Tp = BlastProgramSelector<p>;
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:122:38: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-fpermissive]
122 | return argConv2(options, Tp(), TUnred());
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:122:44: error: there are no arguments to ‘TUnred’ that depend on a template parameter, so a declaration of ‘TUnred’ must be available [-fpermissive]
122 | return argConv2(options, Tp(), TUnred());
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:124:38: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-fpermissive]
124 | return argConv2(options, Tp(), ReducedAminoAcid<Murphy10>());
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:124:44: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’?
124 | return argConv2(options, Tp(), ReducedAminoAcid<Murphy10>());
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:439:15: error: ‘seeds’ was not declared in this scope
439 | clear(seeds);
| ^~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:439:9: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-fpermissive]
439 | clear(seeds);
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:124:61: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’?
124 | return argConv2(options, Tp(), ReducedAminoAcid<Murphy10>());
| ^~~~~~~~
| seqan2::Murphy10
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here
85 | typedef Tag<Murphy10_> Murphy10;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:124:71: error: expected primary-expression before ‘)’ token
124 | return argConv2(options, Tp(), ReducedAminoAcid<Murphy10>());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:141:11: error: ‘BlastProgram’ has not been declared
141 | template <BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:145:10: error: ‘BlastProgramSelector’ has not been declared
145 | BlastProgramSelector<p> const &,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:145:30: error: expected ‘,’ or ‘...’ before ‘<’ token
145 | BlastProgramSelector<p> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: In function ‘int argConv2(const LambdaIndexerOptions&, int)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:149:34: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
149 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), RadixSortSACreateTag());
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:149:55: error: ‘p’ was not declared in this scope
149 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), RadixSortSACreateTag());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:149:58: error: expected primary-expression before ‘)’ token
149 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), RadixSortSACreateTag());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:151:34: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
151 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), Nothing());
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:440:15: error: ‘seedIndex’ was not declared in this scope
440 | clear(seedIndex);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/holders.hpp:440:9: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-fpermissive]
440 | clear(seedIndex);
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:151:55: error: ‘p’ was not declared in this scope
151 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), Nothing());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:151:58: error: expected primary-expression before ‘)’ token
151 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), Nothing());
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:151:73: error: there are no arguments to ‘Nothing’ that depend on a template parameter, so a declaration of ‘Nothing’ must be available [-fpermissive]
151 | return realMain(options, BlastProgramSelector<p>(), TRedAlph(), Nothing());
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:154:11: error: ‘BlastProgram’ has not been declared
154 | template <BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:159:10: error: ‘BlastProgramSelector’ has not been declared
159 | BlastProgramSelector<p> const &,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:159:30: error: expected ‘,’ or ‘...’ before ‘<’ token
159 | BlastProgramSelector<p> const &,
| ^
In file included from /<<PKGBUILDDIR>>/src/lambda.hpp:43,
from /<<PKGBUILDDIR>>/src/lambda.cpp:34:
/<<PKGBUILDDIR>>/src/misc.hpp: At global scope:
/<<PKGBUILDDIR>>/src/misc.hpp:80:18: error: ‘Iter’ does not name a type
80 | const Iter<const String<SimpleType<unsigned char,TAlph>,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:80:22: error: expected ‘,’ or ‘...’ before ‘<’ token
80 | const Iter<const String<SimpleType<unsigned char,TAlph>,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp: In function ‘int realMain(const LambdaIndexerOptions&, int)’:
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:163:23: error: ‘TCDStringSet’ does not name a type
163 | using TOrigSet = TCDStringSet<String<OrigSubjAlph<p>>>;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp: In function ‘std::basic_ostream<char>& operator<<(std::basic_ostream<char>&, int)’:
/<<PKGBUILDDIR>>/src/misc.hpp:84:13: error: ‘it’ was not declared in this scope; did you mean ‘int’?
84 | out << *it;
| ^~
| int
/<<PKGBUILDDIR>>/src/misc.hpp: At global scope:
/<<PKGBUILDDIR>>/src/misc.hpp:145:17: error: ‘Gaps’ was not declared in this scope; did you mean ‘seqan2::Gaps’?
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^~~~
| seqan2::Gaps
In file included from /usr/include/seqan/align.h:82:
/usr/include/seqan/align/gaps_base.h:144:7: note: ‘seqan2::Gaps’ declared here
144 | class Gaps;
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:145:30: error: expected primary-expression before ‘,’ token
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:145:42: error: expected primary-expression before ‘>’ token
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:164:23: error: ‘TCDStringSet’ does not name a type
164 | using TTransSet = TCDStringSet<String<TransAlph<p>>>;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:145:46: error: ‘row0’ was not declared in this scope
145 | localAlignment2(Gaps<TSource0, TGapsSpec0> & row0,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:146:17: error: ‘Gaps’ was not declared in this scope; did you mean ‘seqan2::Gaps’?
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^~~~
| seqan2::Gaps
/usr/include/seqan/align/gaps_base.h:144:7: note: ‘seqan2::Gaps’ declared here
144 | class Gaps;
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:146:30: error: expected primary-expression before ‘,’ token
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:146:42: error: expected primary-expression before ‘>’ token
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:166:5: error: ‘TTransSet’ was not declared in this scope
166 | TTransSet translatedSeqs;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:146:46: error: ‘row1’ was not declared in this scope
146 | Gaps<TSource1, TGapsSpec1> & row1,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:147:17: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^~~~~
| seqan2::Score
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:147:34: error: expected primary-expression before ‘,’ token
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:147:46: error: expected primary-expression before ‘>’ token
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:147:48: error: expected primary-expression before ‘const’
147 | Score<TScoreValue, TScoreSpec> const & scoringScheme,
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:148:17: error: expected primary-expression before ‘int’
148 | int const lowerDiag,
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:149:17: error: expected primary-expression before ‘int’
149 | int const upperDiag,
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:150:31: error: expected primary-expression before ‘&’ token
150 | TAlignContext & alignContext)
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:169:9: error: ‘TOrigSet’ was not declared in this scope
169 | TOrigSet originalSeqs;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:173:33: error: missing template arguments before ‘(’ token
173 | ret = loadSubjSeqsAndIds(originalSeqs, options);
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:150:33: error: ‘alignContext’ was not declared in this scope; did you mean ‘TAlignContext’?
150 | TAlignContext & alignContext)
| ^~~~~~~~~~~~
| TAlignContext
/<<PKGBUILDDIR>>/src/misc.hpp:150:46: error: expected ‘;’ before ‘{’ token
150 | TAlignContext & alignContext)
| ^
| ;
151 | {
| ~
/<<PKGBUILDDIR>>/src/misc.hpp:187:1: error: variable or field ‘readRecords’ declared void
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:13: error: ‘TCDStringSet’ was not declared in this scope; did you mean ‘TSeqStringSet’?
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~~~~~~~~
| TSeqStringSet
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:173:34: error: ‘originalSeqs’ was not declared in this scope
173 | ret = loadSubjSeqsAndIds(originalSeqs, options);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:33: error: expected primary-expression before ‘char’
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:39: error: ‘Alloc’ was not declared in this scope; did you mean ‘seqan2::Alloc’?
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~~
| seqan2::Alloc
/usr/include/seqan/sequence/string_base.h:59:8: note: ‘seqan2::Alloc’ declared here
59 | struct Alloc {};
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:54: error: expected primary-expression before ‘>>’ token
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:187:56: error: expected primary-expression before ‘>’ token
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:178:27: error: ‘p’ was not declared in this scope
178 | if (sIsTranslated(p))
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:178:13: error: there are no arguments to ‘sIsTranslated’ that depend on a template parameter, so a declaration of ‘sIsTranslated’ must be available [-fpermissive]
178 | if (sIsTranslated(p))
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:182:34: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
182 | ret = convertMaskingFile(length(originalSeqs), options);
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:187:60: error: ‘meta’ was not declared in this scope
187 | readRecords(TCDStringSet<String<char, Alloc<Truncate_>>> & meta,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:188:27: error: expected primary-expression before ‘&’ token
188 | TSeqStringSet & seq,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:188:29: error: ‘seq’ was not declared in this scope; did you mean ‘__pstl::execution::v1::seq’?
188 | TSeqStringSet & seq,
| ^~~
| __pstl::execution::v1::seq
In file included from /usr/include/c++/14/pstl/glue_algorithm_defs.h:15,
from /usr/include/c++/14/algorithm:86,
from /usr/include/seqan/basic/debug_test_system.h:156,
from /usr/include/seqan/basic/basic_debug.h:52,
from /usr/include/seqan/basic.h:49:
/usr/include/c++/14/pstl/execution_defs.h:42:46: note: ‘__pstl::execution::v1::seq’ declared here
42 | _GLIBCXX17_INLINE constexpr sequenced_policy seq{};
| ^~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:13: error: ‘FormattedFile’ was not declared in this scope; did you mean ‘seqan2::FormattedFile’?
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~~~~~~~~~~
| seqan2::FormattedFile
/usr/include/seqan/stream/formatted_file.h:213:8: note: ‘seqan2::FormattedFile’ declared here
213 | struct FormattedFile
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:27: error: ‘Fastq’ was not declared in this scope; did you mean ‘seqan2::Fastq’?
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~~
| seqan2::Fastq
In file included from /usr/include/seqan/seq_io.h:52:
/usr/include/seqan/seq_io/fasta_fastq.h:59:24: note: ‘seqan2::Fastq’ declared here
59 | typedef Tag<TagFastq_> Fastq;
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:34: error: ‘Input’ was not declared in this scope; did you mean ‘seqan2::Input’?
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~~
| seqan2::Input
In file included from /usr/include/seqan/file.h:71:
/usr/include/seqan/file/file_interface.h:165:21: note: ‘seqan2::Input’ declared here
165 | typedef Tag<Input_> Input;
| ^~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:189:46: error: expected primary-expression before ‘>’ token
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:189:50: error: ‘file’ was not declared in this scope
189 | FormattedFile<Fastq, Input, TSpec> & file,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:190:19: error: expected primary-expression before ‘maxRecords’
190 | TSize maxRecords)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:187:25: error: ‘translatedSeqs’ was not declared in this scope
187 | translateOrSwap(translatedSeqs, originalSeqs, options);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:187:9: error: there are no arguments to ‘translateOrSwap’ that depend on a template parameter, so a declaration of ‘translateOrSwap’ must be available [-fpermissive]
187 | translateOrSwap(translatedSeqs, originalSeqs, options);
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:15: error: ‘TCDStringSet’ was not declared in this scope
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:35: error: expected primary-expression before ‘char’
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:47: error: expected primary-expression before ‘>>’ token
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:192:28: error: ‘translatedSeqs’ was not declared in this scope
192 | dumpTranslatedSeqs(translatedSeqs, options);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:192:9: error: there are no arguments to ‘dumpTranslatedSeqs’ that depend on a template parameter, so a declaration of ‘dumpTranslatedSeqs’ must be available [-fpermissive]
192 | dumpTranslatedSeqs(translatedSeqs, options);
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:195:24: error: missing template arguments before ‘(’ token
195 | if (!checkIndexSize(translatedSeqs))
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:231:52: error: ‘ids’ was not declared in this scope
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:195:25: error: ‘translatedSeqs’ was not declared in this scope
195 | if (!checkIndexSize(translatedSeqs))
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:15: error: ‘TCDStringSet’ was not declared in this scope
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:200:28: error: ‘TFMIndex’ does not name a type
200 | using TIndexSpec = TFMIndex<TIndexSpecSpec>;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:35: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’?
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~
| seqan2::Dna5
/usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here
134 | typedef SimpleType<unsigned char, Dna5_> Dna5;
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:232:47: error: expected primary-expression before ‘>>’ token
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~
/<<PKGBUILDDIR>>/src/misc.hpp:232:52: error: ‘seqs’ was not declared in this scope
232 | TCDStringSet<String<Dna5, TSpec2>> & seqs,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:233:51: error: expected primary-expression before ‘&’ token
233 | TFile & file)
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:233:53: error: ‘file’ was not declared in this scope
233 | TFile & file)
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:233:57: error: expression list treated as compound expression in initializer [-fpermissive]
233 | TFile & file)
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:233:58: error: expected ‘;’ before ‘{’ token
233 | TFile & file)
| ^
| ;
234 | {
| ~
/<<PKGBUILDDIR>>/src/misc.hpp:258:1: error: redefinition of ‘template<class TSpec1, class TSpec2, class TFile> int myReadRecords’
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:231:1: note: ‘template<class TSpec1, class TSpec2, class TFile> int myReadRecords<TSpec1, TSpec2, TFile>’ previously declared here
231 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:201:9: error: ‘generateIndexAndDump’ was not declared in this scope
201 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:15: error: ‘TCDStringSet’ was not declared in this scope
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:35: error: expected primary-expression before ‘char’
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:258:47: error: expected primary-expression before ‘>>’ token
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:201:30: error: ‘TIndexSpec’ was not declared in this scope; did you mean ‘TIndexSpecSpec’?
201 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^~~~~~~~~~
| TIndexSpecSpec
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:201:55: error: expected primary-expression before ‘>’ token
201 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:258:58: error: ‘ids’ was not declared in this scope
258 | myReadRecords(TCDStringSet<String<char, TSpec1>> & ids,
| ^~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:201:57: error: ‘translatedSeqs’ was not declared in this scope
201 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:203:57: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
203 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:15: error: ‘TCDStringSet’ was not declared in this scope
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:35: error: ‘AminoAcid’ was not declared in this scope; did you mean ‘seqan2::AminoAcid’?
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~~~~~~
| seqan2::AminoAcid
/usr/include/seqan/basic/alphabet_residue.h:550:47: note: ‘seqan2::AminoAcid’ declared here
550 | typedef SimpleType<unsigned char, AminoAcid_> AminoAcid;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:52: error: expected primary-expression before ‘>>’ token
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:203:78: error: ‘p’ was not declared in this scope
203 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:203:81: error: expected primary-expression before ‘)’ token
203 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:207:28: error: ‘IndexSa’ does not name a type
207 | using TIndexSpec = IndexSa<TIndexSpecSpec>;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/misc.hpp:259:58: error: ‘seqs’ was not declared in this scope
259 | TCDStringSet<String<AminoAcid, TSpec2>> & seqs,
| ^~~~
/<<PKGBUILDDIR>>/src/misc.hpp:260:57: error: expected primary-expression before ‘&’ token
260 | TFile & file)
| ^
/<<PKGBUILDDIR>>/src/misc.hpp:260:59: error: ‘file’ was not declared in this scope
260 | TFile & file)
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:54:11: error: ‘BlastProgram’ has not been declared
54 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:55:11: error: ‘BlastTabularSpec’ has not been declared
55 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:79:19: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
79 | public ::std::binary_function < TSav, TSav, bool >
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:101:11: error: ‘BlastTabularSpec’ has not been declared
101 | template <BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:102:11: error: ‘BlastProgram’ has not been declared
102 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:107:71: error: ‘p’ was not declared in this scope
107 | prepareScoringMore(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:208:9: error: ‘generateIndexAndDump’ was not declared in this scope
208 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:107:74: error: ‘h’ was not declared in this scope
107 | prepareScoringMore(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:107:75: error: template argument 4 is invalid
107 | prepareScoringMore(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:107:75: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void prepareScoringMore(int&, const LambdaOptions&, const std::true_type&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:111:40: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
111 | setScoreMatch(context(globalHolder.outfile).scoringScheme, options.match);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:111:19: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
111 | setScoreMatch(context(globalHolder.outfile).scoringScheme, options.match);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:112:43: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
112 | setScoreMismatch(context(globalHolder.outfile).scoringScheme, options.misMatch);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:112:22: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
112 | setScoreMismatch(context(globalHolder.outfile).scoringScheme, options.misMatch);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.hpp:115:11: error: ‘BlastTabularSpec’ has not been declared
115 | template <BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:116:11: error: ‘BlastProgram’ has not been declared
116 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:208:30: error: ‘TIndexSpec’ was not declared in this scope; did you mean ‘TIndexSpecSpec’?
208 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^~~~~~~~~~
| TIndexSpecSpec
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:208:55: error: expected primary-expression before ‘>’ token
208 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:121:71: error: ‘p’ was not declared in this scope
121 | prepareScoringMore(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:121:74: error: ‘h’ was not declared in this scope
121 | prepareScoringMore(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:121:75: error: template argument 4 is invalid
121 | prepareScoringMore(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:121:75: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void prepareScoringMore(int&, const LambdaOptions&, const std::false_type&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:130:53: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
130 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:130:32: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
130 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:131:32: error: ‘AminoAcidScoreMatrixID’ has not been declared
131 | AminoAcidScoreMatrixID::BLOSUM45);
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:134:53: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
134 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:134:32: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
134 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:135:32: error: ‘AminoAcidScoreMatrixID’ has not been declared
135 | AminoAcidScoreMatrixID::BLOSUM62);
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:138:53: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
138 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:138:32: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
138 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:139:32: error: ‘AminoAcidScoreMatrixID’ has not been declared
139 | AminoAcidScoreMatrixID::BLOSUM80);
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.hpp:146:11: error: ‘BlastTabularSpec’ has not been declared
146 | template <BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:147:11: error: ‘BlastProgram’ has not been declared
147 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:152:67: error: ‘p’ was not declared in this scope
152 | prepareScoring(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:208:57: error: ‘translatedSeqs’ was not declared in this scope
208 | generateIndexAndDump<TIndexSpec,TIndexSpecSpec>(translatedSeqs,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:210:57: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
210 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:152:70: error: ‘h’ was not declared in this scope
152 | prepareScoring(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:152:71: error: template argument 4 is invalid
152 | prepareScoring(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:152:71: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:210:78: error: ‘p’ was not declared in this scope
210 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda_indexer.cpp:210:81: error: expected primary-expression before ‘)’ token
210 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int prepareScoring(int&, const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:155:78: error: ‘p’ was not declared in this scope
155 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:155:81: error: ‘h’ was not declared in this scope
155 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:155:82: error: template argument 4 is invalid
155 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:155:82: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp:158:92: error: wrong number of template arguments (1, should be 2)
158 | std::is_same<typename TGlobalHolder::TScoreScheme, Score<int, Simple>>());
| ^~
/usr/include/c++/14/type_traits:780:12: note: provided for ‘template<class, class> struct std::is_same’
780 | struct is_same;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:160:47: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
160 | setScoreGapOpenBlast(context(globalHolder.outfile).scoringScheme, options.gapOpen);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:160:26: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
160 | setScoreGapOpenBlast(context(globalHolder.outfile).scoringScheme, options.gapOpen);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:161:44: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
161 | setScoreGapExtend(context(globalHolder.outfile).scoringScheme, options.gapExtend);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:161:23: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
161 | setScoreGapExtend(context(globalHolder.outfile).scoringScheme, options.gapExtend);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:163:39: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
163 | if (!isValid(context(globalHolder.outfile).scoringScheme))
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:163:18: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
163 | if (!isValid(context(globalHolder.outfile).scoringScheme))
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.hpp:176:11: error: ‘BlastTabularSpec’ has not been declared
176 | template <BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:177:11: error: ‘BlastProgram’ has not been declared
177 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:182:65: error: ‘p’ was not declared in this scope
182 | loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:182:68: error: ‘h’ was not declared in this scope
182 | loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:182:69: error: template argument 4 is invalid
182 | loadSubjects(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:182:69: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int loadSubjects(int&, const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:185:68: error: ‘p’ was not declared in this scope
185 | using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:185:71: error: ‘h’ was not declared in this scope
185 | using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:185:72: error: template argument 4 is invalid
185 | using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:185:72: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp:190:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’?
190 | CharString _dbSeqs;
| ^~~~~~~~~~
| seqan2::CharString
In file included from /usr/include/seqan/sequence.h:112:
/usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here
55 | typedef String<char, Alloc<void> > CharString;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:192:9: error: ‘TGH’ has not been declared
192 | if (TGH::indexIsFM || TGH::alphReduction) // otherwise sequences are loaded as part of index
| ^~~
/<<PKGBUILDDIR>>/src/lambda.hpp:192:27: error: ‘TGH’ has not been declared
192 | if (TGH::indexIsFM || TGH::alphReduction) // otherwise sequences are loaded as part of index
| ^~~
/<<PKGBUILDDIR>>/src/lambda.hpp:194:17: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
194 | start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:198:9: error: ‘_dbSeqs’ was not declared in this scope
198 | _dbSeqs = options.dbFile;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:199:9: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
199 | append(_dbSeqs, ".");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:200:35: error: ‘TransAlph’ was not declared in this scope
200 | append(_dbSeqs, _alphName(TransAlph<p>()));
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:200:48: error: expected primary-expression before ‘)’ token
200 | append(_dbSeqs, _alphName(TransAlph<p>()));
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:200:49: error: ‘_alphName’ cannot be used as a function
200 | append(_dbSeqs, _alphName(TransAlph<p>()));
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:200:9: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
200 | append(_dbSeqs, _alphName(TransAlph<p>()));
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:202:33: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’
202 | ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:202:43: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
202 | ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:202:63: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’?
202 | ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~~~~
| seqan2::OPEN_RDONLY
/usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here
149 | OPEN_RDONLY = 1,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:210:33: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’
210 | if (length(globalHolder.subjSeqs) == 0)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:210:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
210 | if (length(globalHolder.subjSeqs) == 0)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:216:13: error: ‘TGH’ has not been declared
216 | if (TGH::alphReduction)
| ^~~
/<<PKGBUILDDIR>>/src/lambda.hpp:217:26: error: request for member ‘redSubjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’
217 | globalHolder.redSubjSeqs.limits = globalHolder.subjSeqs.limits;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:217:60: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’
217 | globalHolder.redSubjSeqs.limits = globalHolder.subjSeqs.limits;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:219:18: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
219 | finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:222:37: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’
222 | length(globalHolder.subjSeqs), "\n\n");
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:222:17: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
222 | length(globalHolder.subjSeqs), "\n\n");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:225:13: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
225 | start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:229:5: error: ‘_dbSeqs’ was not declared in this scope
229 | _dbSeqs = options.dbFile;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:230:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
230 | append(_dbSeqs, ".ids");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:231:29: error: request for member ‘subjIds’ in ‘globalHolder’, which is of non-class type ‘int’
231 | ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:231:38: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
231 | ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:231:58: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’?
231 | ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~~~~
| seqan2::OPEN_RDONLY
/usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here
149 | OPEN_RDONLY = 1,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:238:14: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
238 | finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:242:26: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’
242 | context(globalHolder.outfile).dbName = options.dbFile;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:242:5: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-fpermissive]
242 | context(globalHolder.outfile).dbName = options.dbFile;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:246:9: error: there are no arguments to ‘sIsTranslated’ that depend on a template parameter, so a declaration of ‘sIsTranslated’ must be available [-fpermissive]
246 | if (sIsTranslated(p))
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:248:17: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
248 | start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:253:9: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
253 | append(_dbSeqs, ".untranslengths");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:254:33: error: request for member ‘untransSubjSeqLengths’ in ‘globalHolder’, which is of non-class type ‘int’
254 | ret = open(globalHolder.untransSubjSeqLengths, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:254:56: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
254 | ret = open(globalHolder.untransSubjSeqLengths, toCString(_dbSeqs), OPEN_RDONLY);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:262:18: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
262 | finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int loadDbIndexFromDisk(TGlobalHolder&, const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:281:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
281 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:282:24: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
282 | std::string path = toCString(options.dbFile);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:290:39: error: ‘BlastProgram’ has not been declared
290 | if ((globalHolder.blastProgram != BlastProgram::BLASTN) && // BLASTN indexes are compatible
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:291:54: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
291 | ((TGlobalHolder::alphReduction && fileExists(toCString(path + ".txt.concat"))) ||
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:292:83: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
292 | (!TGlobalHolder::alphReduction && TGlobalHolder::indexIsFM && !fileExists(toCString(path + ".lf.drv.wtc.24")))))
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:301:56: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’?
301 | int ret = open(globalHolder.dbIndex, path.c_str(), OPEN_RDONLY);
| ^~~~~~~~~~~
| seqan2::OPEN_RDONLY
/usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here
149 | OPEN_RDONLY = 1,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:315:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
315 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.hpp:339:11: error: ‘BlastTabularSpec’ has not been declared
339 | template <BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:340:11: error: ‘BlastProgram’ has not been declared
340 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:345:69: error: ‘p’ was not declared in this scope
345 | loadSegintervals(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:345:72: error: ‘h’ was not declared in this scope
345 | loadSegintervals(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:345:73: error: template argument 4 is invalid
345 | loadSegintervals(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:345:73: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int loadSegintervals(int&, const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:349:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
349 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:353:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’?
353 | CharString segFileS = options.dbFile;
| ^~~~~~~~~~
| seqan2::CharString
/usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here
55 | typedef String<char, Alloc<void> > CharString;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:354:12: error: ‘segFileS’ was not declared in this scope
354 | append(segFileS, ".binseg_s.concat");
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:354:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
354 | append(segFileS, ".binseg_s.concat");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:355:15: error: expected ‘;’ before ‘segFileE’
355 | CharString segFileE = options.dbFile;
| ^~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/lambda.hpp:356:12: error: ‘segFileE’ was not declared in this scope
356 | append(segFileE, ".binseg_e.concat");
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:356:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-fpermissive]
356 | append(segFileE, ".binseg_e.concat");
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:360:15: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
360 | if ((stat(toCString(segFileS), &buffer) == 0) &&
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:361:15: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
361 | (stat(toCString(segFileE), &buffer) == 0))
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:364:26: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
364 | resize(segFileS, length(segFileS) - 7);
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:365:26: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
365 | resize(segFileE, length(segFileE) - 7);
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:367:35: error: request for member ‘segIntStarts’ in ‘globalHolder’, which is of non-class type ‘int’
367 | fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:367:49: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
367 | fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:367:70: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’?
367 | fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY);
| ^~~~~~~~~~~
| seqan2::OPEN_RDONLY
/usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here
149 | OPEN_RDONLY = 1,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:369:39: error: request for member ‘segIntEnds’ in ‘globalHolder’, which is of non-class type ‘int’
369 | fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY);
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:369:51: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-fpermissive]
369 | fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:382:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
382 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.hpp:398:1: error: variable or field ‘loadQueryImplTrans’ declared void
398 | loadQueryImplTrans(TCDStringSet<String<TTargetAlph, TSpec1>> & target,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:398:20: error: ‘TCDStringSet’ was not declared in this scope
398 | loadQueryImplTrans(TCDStringSet<String<TTargetAlph, TSpec1>> & target,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:398:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
398 | loadQueryImplTrans(TCDStringSet<String<TTargetAlph, TSpec1>> & target,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:398:51: error: expected primary-expression before ‘,’ token
398 | loadQueryImplTrans(TCDStringSet<String<TTargetAlph, TSpec1>> & target,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:398:59: error: expected primary-expression before ‘>>’ token
398 | loadQueryImplTrans(TCDStringSet<String<TTargetAlph, TSpec1>> & target,
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:398:64: error: ‘target’ was not declared in this scope; did you mean ‘seqan2::target’?
398 | loadQueryImplTrans(TCDStringSet<String<TTargetAlph, TSpec1>> & target,
| ^~~~~~
| seqan2::target
In file included from /usr/include/seqan/graph_types.h:48,
from /usr/include/seqan/graph_align.h:47:
/usr/include/seqan/graph_types/graph_edgestump.h:552:1: note: ‘seqan2::target’ declared here
552 | target(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:399:20: error: ‘TCDStringSet’ was not declared in this scope
399 | TCDStringSet<String<TSourceAlph, TSpec2>> & source,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:399:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
399 | TCDStringSet<String<TSourceAlph, TSpec2>> & source,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:399:51: error: expected primary-expression before ‘,’ token
399 | TCDStringSet<String<TSourceAlph, TSpec2>> & source,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:399:59: error: expected primary-expression before ‘>>’ token
399 | TCDStringSet<String<TSourceAlph, TSpec2>> & source,
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:399:64: error: ‘source’ was not declared in this scope; did you mean ‘seqan2::source’?
399 | TCDStringSet<String<TSourceAlph, TSpec2>> & source,
| ^~~~~~
| seqan2::source
In file included from /usr/include/seqan/pipe.h:56,
from /usr/include/seqan/index.h:42,
from /<<PKGBUILDDIR>>/src/options.hpp:33:
/usr/include/seqan/pipe/pipe_base.h:362:5: note: ‘seqan2::source’ declared here
362 | source(Pipe<TInput, TSpec> &me) {
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:400:63: error: expected primary-expression before ‘&’ token
400 | TUntransLengths & untransQrySeqLengths,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:400:65: error: ‘untransQrySeqLengths’ was not declared in this scope
400 | TUntransLengths & untransQrySeqLengths,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:401:57: error: expected primary-expression before ‘const’
401 | LambdaOptions const & options)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:1: error: variable or field ‘loadQueryImplTrans’ declared void
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:20: error: ‘TCDStringSet’ was not declared in this scope
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:40: error: ‘TransAlph’ was not declared in this scope
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:50: error: ‘BlastProgram’ has not been declared
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:71: error: expected primary-expression before ‘,’ token
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:432:79: error: expected primary-expression before ‘>>’ token
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:432:84: error: ‘target’ was not declared in this scope; did you mean ‘seqan2::target’?
432 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec1>> & target,
| ^~~~~~
| seqan2::target
/usr/include/seqan/graph_types/graph_edgestump.h:552:1: note: ‘seqan2::target’ declared here
552 | target(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:433:20: error: ‘TCDStringSet’ was not declared in this scope
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:433:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:433:40: error: ‘TransAlph’ was not declared in this scope
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:433:50: error: ‘BlastProgram’ has not been declared
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:433:71: error: expected primary-expression before ‘,’ token
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:433:79: error: expected primary-expression before ‘>>’ token
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:433:84: error: ‘source’ was not declared in this scope; did you mean ‘seqan2::source’?
433 | TCDStringSet<String<TransAlph<BlastProgram::BLASTN>, TSpec2>> & source,
| ^~~~~~
| seqan2::source
/usr/include/seqan/pipe/pipe_base.h:362:5: note: ‘seqan2::source’ declared here
362 | source(Pipe<TInput, TSpec> &me) {
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:434:83: error: expected primary-expression before ‘&’ token
434 | TUntransLengths & /**/,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:434:89: error: expected primary-expression before ‘,’ token
434 | TUntransLengths & /**/,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:435:77: error: expected primary-expression before ‘const’
435 | LambdaOptions const & options)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:1: error: variable or field ‘loadQueryImplTrans’ declared void
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:20: error: ‘TCDStringSet’ was not declared in this scope
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:40: error: ‘TransAlph’ was not declared in this scope
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:50: error: ‘BlastProgram’ has not been declared
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:71: error: expected primary-expression before ‘,’ token
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:476:79: error: expected primary-expression before ‘>>’ token
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:476:84: error: ‘target’ was not declared in this scope; did you mean ‘seqan2::target’?
476 | loadQueryImplTrans(TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec1>> & target,
| ^~~~~~
| seqan2::target
/usr/include/seqan/graph_types/graph_edgestump.h:552:1: note: ‘seqan2::target’ declared here
552 | target(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:477:20: error: ‘TCDStringSet’ was not declared in this scope
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:477:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:477:40: error: ‘TransAlph’ was not declared in this scope
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:477:50: error: ‘BlastProgram’ has not been declared
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:477:71: error: expected primary-expression before ‘,’ token
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:477:79: error: expected primary-expression before ‘>>’ token
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:477:84: error: ‘source’ was not declared in this scope; did you mean ‘seqan2::source’?
477 | TCDStringSet<String<TransAlph<BlastProgram::BLASTP>, TSpec2>> & source,
| ^~~~~~
| seqan2::source
/usr/include/seqan/pipe/pipe_base.h:362:5: note: ‘seqan2::source’ declared here
362 | source(Pipe<TInput, TSpec> &me) {
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:478:46: error: expected primary-expression before ‘&’ token
478 | TUntransLengths & /**/,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:478:52: error: expected primary-expression before ‘,’ token
478 | TUntransLengths & /**/,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:479:40: error: expected primary-expression before ‘const’
479 | LambdaOptions const & /**/)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:485:11: error: ‘BlastTabularSpec’ has not been declared
485 | template <BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:486:11: error: ‘BlastProgram’ has not been declared
486 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:491:62: error: ‘p’ was not declared in this scope
491 | loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:491:65: error: ‘h’ was not declared in this scope
491 | loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:491:66: error: template argument 4 is invalid
491 | loadQuery(GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h> & globalHolder,
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:491:66: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int loadQuery(int&, const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:494:68: error: ‘p’ was not declared in this scope
494 | using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:494:71: error: ‘h’ was not declared in this scope
494 | using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:494:72: error: template argument 4 is invalid
494 | using TGH = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:494:72: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.hpp:495:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
495 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:500:5: error: ‘TCDStringSet’ was not declared in this scope
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:500:18: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’?
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^~~~~~
| seqan2::String
/usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here
290 | class String;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:500:25: error: ‘OrigQryAlph’ was not declared in this scope
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:500:39: error: expected primary-expression before ‘,’ token
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:500:50: error: ‘TGH’ has not been declared
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^~~
/<<PKGBUILDDIR>>/src/lambda.hpp:500:62: error: expected ‘(’ before ‘>>’ token
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^~
| (
/<<PKGBUILDDIR>>/src/lambda.hpp:500:65: error: ‘origSeqs’ was not declared in this scope
500 | TCDStringSet<String<OrigQryAlph<p>, typename TGH::TQryTag>> origSeqs;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:505:9: error: ‘SeqFileIn’ was not declared in this scope; did you mean ‘seqan2::SeqFileIn’?
505 | SeqFileIn infile(toCString(options.queryFile));
| ^~~~~~~~~
| seqan2::SeqFileIn
In file included from /usr/include/seqan/seq_io.h:61:
/usr/include/seqan/seq_io/sequence_file.h:59:41: note: ‘seqan2::SeqFileIn’ declared here
59 | typedef FormattedFile<Fastq, Input> SeqFileIn;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:506:32: error: missing template arguments before ‘(’ token
506 | int ret = myReadRecords(globalHolder.qryIds, origSeqs, infile);
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:506:46: error: request for member ‘qryIds’ in ‘globalHolder’, which is of non-class type ‘int’
506 | int ret = myReadRecords(globalHolder.qryIds, origSeqs, infile);
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:506:64: error: ‘infile’ was not declared in this scope; did you mean ‘inline’?
506 | int ret = myReadRecords(globalHolder.qryIds, origSeqs, infile);
| ^~~~~~
| inline
/<<PKGBUILDDIR>>/src/lambda.hpp:510:11: error: ‘IOError’ does not name a type
510 | catch(IOError const & e)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:510:18: error: expected ‘)’ before ‘const’
510 | catch(IOError const & e)
| ~ ^~~~~~
| )
/<<PKGBUILDDIR>>/src/lambda.hpp:510:19: error: expected ‘{’ before ‘const’
510 | catch(IOError const & e)
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:510:28: error: expected initializer before ‘)’ token
510 | catch(IOError const & e)
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:518:37: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
518 | loadQueryImplTrans(globalHolder.qrySeqs,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:520:37: error: request for member ‘untransQrySeqLengths’ in ‘globalHolder’, which is of non-class type ‘int’
520 | globalHolder.untransQrySeqLengths,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:518:5: error: there are no arguments to ‘loadQueryImplTrans’ that depend on a template parameter, so a declaration of ‘loadQueryImplTrans’ must be available [-fpermissive]
518 | loadQueryImplTrans(globalHolder.qrySeqs,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:524:36: error: request for member ‘blastProgram’ in ‘globalHolder’, which is of non-class type ‘int’
524 | if (qIsTranslated(globalHolder.blastProgram) && (options.outFileFormat > 0) &&
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:524:9: error: there are no arguments to ‘qIsTranslated’ that depend on a template parameter, so a declaration of ‘qIsTranslated’ must be available [-fpermissive]
524 | if (qIsTranslated(globalHolder.blastProgram) && (options.outFileFormat > 0) &&
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:526:42: error: request for member ‘untranslatedQrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
526 | std::swap(origSeqs, globalHolder.untranslatedQrySeqs);
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:528:9: error: ‘TGH’ has not been declared
528 | if (TGH::alphReduction)
| ^~~
/<<PKGBUILDDIR>>/src/lambda.hpp:529:22: error: request for member ‘redQrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
529 | globalHolder.redQrySeqs.limits = globalHolder.qrySeqs.limits;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:529:55: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
529 | globalHolder.redQrySeqs.limits = globalHolder.qrySeqs.limits;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:531:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
531 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:535:40: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
535 | for (auto const & s : globalHolder.qrySeqs)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:536:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
536 | if (length(s) > maxLen)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:537:22: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
537 | maxLen = length(s);
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:541:33: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
541 | length(globalHolder.qrySeqs), "\nLongest query sequence: ",
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:541:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
541 | length(globalHolder.qrySeqs), "\nLongest query sequence: ",
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:544:29: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
544 | if (length(globalHolder.qrySeqs) == 0)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:544:9: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
544 | if (length(globalHolder.qrySeqs) == 0)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:550:29: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’
550 | if (length(globalHolder.qrySeqs) >= std::numeric_limits<typename TGH::TMatch::TQId>::max())
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:550:9: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
550 | if (length(globalHolder.qrySeqs) >= std::numeric_limits<typename TGH::TMatch::TQId>::max())
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:550:87: error: template argument 1 is invalid
550 | if (length(globalHolder.qrySeqs) >= std::numeric_limits<typename TGH::TMatch::TQId>::max())
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:553:68: error: template argument 1 is invalid
553 | << std::numeric_limits<typename TGH::TMatch::TQId>::max()
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:558:65: error: template argument 1 is invalid
558 | if (maxLen >= std::numeric_limits<typename TGH::TMatch::TPos>::max())
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:561:96: error: template argument 1 is invalid
561 | << "The maximum length is " << std::numeric_limits<typename TGH::TMatch::TPos>::max()
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int generateSeeds(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:590:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
590 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:602:25: error: there are no arguments to ‘Generous’ that depend on a template parameter, so a declaration of ‘Generous’ must be available [-fpermissive]
602 | Generous());
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:603:42: error: there are no arguments to ‘Generous’ that depend on a template parameter, so a declaration of ‘Generous’ must be available [-fpermissive]
603 | appendValue(lH.seedRefs, i, Generous());
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:604:42: error: there are no arguments to ‘Generous’ that depend on a template parameter, so a declaration of ‘Generous’ must be available [-fpermissive]
604 | appendValue(lH.seedRanks, j, Generous());
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:609:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
609 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int generateTrieOverSeeds(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:638:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
638 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:640:22: error: expected nested-name-specifier before ‘Fibre’
640 | typedef typename Fibre<typename TLocalHolder::TSeedIndex, EsaSA>::Type TSa;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:640:27: error: expected initializer before ‘<’ token
640 | typedef typename Fibre<typename TLocalHolder::TSeedIndex, EsaSA>::Type TSa;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:643:5: error: ‘TSa’ was not declared in this scope
643 | TSa & sa = indexSA(lH.seedIndex);
| ^~~
/<<PKGBUILDDIR>>/src/lambda.hpp:643:11: error: ‘sa’ was not declared in this scope
643 | TSa & sa = indexSA(lH.seedIndex);
| ^~
/<<PKGBUILDDIR>>/src/lambda.hpp:647:23: error: there are no arguments to ‘value’ that depend on a template parameter, so a declaration of ‘value’ must be available [-fpermissive]
647 | assignValueI1(value(sa,u), u);
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:648:23: error: there are no arguments to ‘value’ that depend on a template parameter, so a declaration of ‘value’ must be available [-fpermissive]
648 | assignValueI2(value(sa,u), 0);
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:650:72: error: wrong number of template arguments (1, should be 2)
650 | Comp<typename Value<TSa>::Type, typename TLocalHolder::TSeeds const> comp(lH.seeds);
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:78:8: note: provided for ‘template<class TSav, class TStringSet> struct Comp’
78 | struct Comp :
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:651:25: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
651 | std::sort(begin(sa, Standard()), end(sa, Standard()), comp);
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:651:46: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-fpermissive]
651 | std::sort(begin(sa, Standard()), end(sa, Standard()), comp);
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:652:14: error: expected nested-name-specifier before ‘Iterator’
652 | typename Iterator<typename TLocalHolder::TSeedIndex, TopDown<> >::Type it(lH.seedIndex); // instantiate
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:652:14: error: expected ‘(’ before ‘Iterator’
652 | typename Iterator<typename TLocalHolder::TSeedIndex, TopDown<> >::Type it(lH.seedIndex); // instantiate
| ^~~~~~~~
| (
/<<PKGBUILDDIR>>/src/lambda.hpp:653:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
653 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:659:24: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
659 | length(sa), " fibres in SeedIndex. ");;
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void __searchDoubleIndex(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:811:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
811 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:813:26: error: ‘Finder_’ does not name a type
813 | using LambdaFinder = Finder_<decltype(lH.gH.dbIndex),
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:819:5: error: ‘LambdaFinder’ was not declared in this scope
819 | LambdaFinder finder;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:821:28: error: ‘LambdaFinder’ is not a type
821 | auto delegate = [&lH] (LambdaFinder const & finder)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In lambda function:
/<<PKGBUILDDIR>>/src/lambda.hpp:823:51: error: request for member ‘patternStack’ in ‘finder’, which is of non-class type ‘const int’
823 | auto qryOccs = getOccurrences(back(finder.patternStack));
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:823:39: error: there are no arguments to ‘back’ that depend on a template parameter, so a declaration of ‘back’ must be available [-fpermissive]
823 | auto qryOccs = getOccurrences(back(finder.patternStack));
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:824:52: error: request for member ‘textStack’ in ‘finder’, which is of non-class type ‘const int’
824 | auto subjOccs = getOccurrences(back(finder.textStack));
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:824:40: error: there are no arguments to ‘back’ that depend on a template parameter, so a declaration of ‘back’ must be available [-fpermissive]
824 | auto subjOccs = getOccurrences(back(finder.textStack));
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void __searchDoubleIndex(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:833:11: error: ‘finder’ was not declared in this scope; did you mean ‘rindex’?
833 | _find(finder, lH.gH.dbIndex, lH.seedIndex, lH.options.maxSeedDist, delegate);
| ^~~~~~
| rindex
/<<PKGBUILDDIR>>/src/lambda.hpp:835:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
835 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void __searchSingleIndex(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:847:22: error: expected nested-name-specifier before ‘Iterator’
847 | typedef typename Iterator<decltype(lH.seeds) const, Rooted>::Type TSeedsIt;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:847:30: error: expected initializer before ‘<’ token
847 | typedef typename Iterator<decltype(lH.seeds) const, Rooted>::Type TSeedsIt;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:848:22: error: expected nested-name-specifier before ‘Iterator’
848 | typedef typename Iterator<decltype(lH.gH.dbIndex),TopDown<>>::Type TIndexIt;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:848:30: error: expected initializer before ‘<’ token
848 | typedef typename Iterator<decltype(lH.gH.dbIndex),TopDown<>>::Type TIndexIt;
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:857:28: error: ‘TIndexIt’ has not been declared
857 | auto delegate = [&lH] (TIndexIt & indexIt,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:858:28: error: ‘TSeedsIt’ has not been declared
858 | TSeedsIt const & seedsIt,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In lambda function:
/<<PKGBUILDDIR>>/src/lambda.hpp:861:23: error: there are no arguments to ‘position’ that depend on a template parameter, so a declaration of ‘position’ must be available [-fpermissive]
861 | auto qryOcc = position(seedsIt);
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:862:25: error: there are no arguments to ‘getOccurrences’ that depend on a template parameter, so a declaration of ‘getOccurrences’ must be available [-fpermissive]
862 | auto subjOccs = getOccurrences(indexIt);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void __searchSingleIndex(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:871:10: error: ‘Backtracking’ was not declared in this scope; did you mean ‘seqan2::Backtracking’?
871 | Backtracking<BackSpec>());
| ^~~~~~~~~~~~
| seqan2::Backtracking
In file included from /usr/include/seqan/index.h:224:
/usr/include/seqan/index/find_backtracking.h:49:8: note: ‘seqan2::Backtracking’ declared here
49 | struct Backtracking;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:871:31: error: expected primary-expression before ‘>’ token
871 | Backtracking<BackSpec>());
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp:871:33: error: expected primary-expression before ‘)’ token
871 | Backtracking<BackSpec>());
| ^
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void search(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:889:18: error: ‘Backtracking’ was not declared in this scope; did you mean ‘seqan2::Backtracking’?
889 | __search<Backtracking<Exact>>(lH);
| ^~~~~~~~~~~~
| seqan2::Backtracking
/usr/include/seqan/index/find_backtracking.h:49:8: note: ‘seqan2::Backtracking’ declared here
49 | struct Backtracking;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:889:31: error: ‘Exact’ was not declared in this scope; did you mean ‘seqan2::Exact’?
889 | __search<Backtracking<Exact>>(lH);
| ^~~~~
| seqan2::Exact
In file included from /usr/include/seqan/sequence.h:94:
/usr/include/seqan/sequence/sequence_interface.h:120:24: note: ‘seqan2::Exact’ declared here
120 | typedef Tag<TagExact_> Exact;
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:891:18: error: ‘Backtracking’ was not declared in this scope; did you mean ‘seqan2::Backtracking’?
891 | __search<Backtracking<HammingDistance>>(lH);
| ^~~~~~~~~~~~
| seqan2::Backtracking
/usr/include/seqan/index/find_backtracking.h:49:8: note: ‘seqan2::Backtracking’ declared here
49 | struct Backtracking;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:891:31: error: ‘HammingDistance’ was not declared in this scope; did you mean ‘seqan2::HammingDistance’?
891 | __search<Backtracking<HammingDistance>>(lH);
| ^~~~~~~~~~~~~~~
| seqan2::HammingDistance
In file included from /usr/include/seqan/basic/basic_fundamental.h:66,
from /usr/include/seqan/basic.h:58:
/usr/include/seqan/basic/fundamental_tags.h:361:37: note: ‘seqan2::HammingDistance’ declared here
361 | typedef Tag<HammingDistance_> HammingDistance;
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘void sortMatches(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:916:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
916 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:934:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
934 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int computeBlastMatch(TBlastMatch&, const typename TLocalHolder::TMatch&, TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:1177:9: error: ‘Tuple’ was not declared in this scope; did you mean ‘seqan2::Tuple’?
1177 | Tuple<decltype(bm.qStart), 4> positions =
| ^~~~~
| seqan2::Tuple
In file included from /usr/include/seqan/basic/basic_aggregate.h:59,
from /usr/include/seqan/basic.h:98:
/usr/include/seqan/basic/tuple_base.h:88:8: note: ‘seqan2::Tuple’ declared here
88 | struct Tuple
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1177:15: error: expected primary-expression before ‘decltype’
1177 | Tuple<decltype(bm.qStart), 4> positions =
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1189:44: error: ‘positions’ was not declared in this scope
1189 | positions,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1190:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’?
1190 | EXTEND_BOTH,
| ^~~~~~~~~~~
| seqan2::EXTEND_BOTH
In file included from /usr/include/seqan/seeds.h:70:
/usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here
128 | EXTEND_BOTH = 3
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1195:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-fpermissive]
1195 | True(),
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1196:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-fpermissive]
1196 | True(),
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1205:44: error: ‘positions’ was not declared in this scope
1205 | positions,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1206:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’?
1206 | EXTEND_BOTH,
| ^~~~~~~~~~~
| seqan2::EXTEND_BOTH
/usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here
128 | EXTEND_BOTH = 3
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1211:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-fpermissive]
1211 | True(),
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1212:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-fpermissive]
1212 | False(),
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1224:44: error: ‘positions’ was not declared in this scope
1224 | positions,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1225:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’?
1225 | EXTEND_BOTH,
| ^~~~~~~~~~~
| seqan2::EXTEND_BOTH
/usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here
128 | EXTEND_BOTH = 3
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1230:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-fpermissive]
1230 | False(),
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1231:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-fpermissive]
1231 | True(),
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1240:44: error: ‘positions’ was not declared in this scope
1240 | positions,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1241:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’?
1241 | EXTEND_BOTH,
| ^~~~~~~~~~~
| seqan2::EXTEND_BOTH
/usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here
128 | EXTEND_BOTH = 3
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1246:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-fpermissive]
1246 | False(),
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1247:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-fpermissive]
1247 | False(),
| ^~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp: In function ‘int iterateMatches(TLocalHolder&)’:
/<<PKGBUILDDIR>>/src/lambda.hpp:1332:27: error: ‘BlastMatch’ does not name a type
1332 | using TBlastMatch = BlastMatch<
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1339:27: error: ‘BlastRecord’ does not name a type
1339 | using TBlastRecord = BlastRecord<TBlastMatch>;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1345:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
1345 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1372:9: error: ‘TBlastRecord’ was not declared in this scope
1372 | TBlastRecord record(lH.gH.qryIds[trueQryId]);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1374:9: error: ‘record’ was not declared in this scope
1374 | record.qLength = (qIsTranslated(lH.gH.blastProgram)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1454:29: error: there are no arguments to ‘back’ that depend on a template parameter, so a declaration of ‘back’ must be available [-fpermissive]
1454 | auto & bm = back(record.matches);
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1611:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
1611 | if (length(record.matches) > 0)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.hpp:1637:25: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
1637 | double finish = sysTime() - start;
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:57:11: error: ‘BlastTabularSpec’ has not been declared
57 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:61:10: error: ‘BlastTabularSpecSelector’ has not been declared
61 | BlastTabularSpecSelector<h> const &);
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:61:34: error: expected ‘,’ or ‘...’ before ‘<’ token
61 | BlastTabularSpecSelector<h> const &);
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:64:11: error: ‘BlastTabularSpec’ has not been declared
64 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:65:11: error: ‘BlastProgram’ has not been declared
65 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:69:10: error: ‘BlastTabularSpecSelector’ has not been declared
69 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:69:34: error: expected ‘,’ or ‘...’ before ‘<’ token
69 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:74:11: error: ‘BlastTabularSpec’ has not been declared
74 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:75:11: error: ‘BlastProgram’ has not been declared
75 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:79:10: error: ‘BlastTabularSpecSelector’ has not been declared
79 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:79:34: error: expected ‘,’ or ‘...’ before ‘<’ token
79 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:86:11: error: ‘BlastTabularSpec’ has not been declared
86 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:87:11: error: ‘BlastProgram’ has not been declared
87 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:91:10: error: ‘BlastTabularSpecSelector’ has not been declared
91 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:91:34: error: expected ‘,’ or ‘...’ before ‘<’ token
91 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:100:11: error: ‘BlastProgram’ has not been declared
100 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:101:11: error: ‘BlastTabularSpec’ has not been declared
101 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:105:10: error: ‘BlastTabularSpecSelector’ has not been declared
105 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:105:34: error: expected ‘,’ or ‘...’ before ‘<’ token
105 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:119:12: error: ‘ArgumentParser’ is not a member of ‘seqan’; did you mean ‘seqan2::ArgumentParser’?
119 | seqan::ArgumentParser parser;
| ^~~~~~~~~~~~~~
/usr/include/seqan/arg_parse/argument_parser.h:152:7: note: ‘seqan2::ArgumentParser’ declared here
152 | class ArgumentParser
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:121:12: error: ‘seqan::ArgumentParser’ has not been declared
121 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:126:9: error: ‘res’ was not declared in this scope
126 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~
/<<PKGBUILDDIR>>/src/lambda.cpp:126:23: error: ‘seqan::ArgumentParser’ has not been declared
126 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:127:30: error: ‘seqan::ArgumentParser’ has not been declared
127 | return res == seqan::ArgumentParser::PARSE_ERROR;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv0(const LambdaOptions&)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:138:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’?
138 | CharString output = options.output;
| ^~~~~~~~~~
| seqan2::CharString
/usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here
55 | typedef String<char, Alloc<void> > CharString;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:139:18: error: ‘output’ was not declared in this scope
139 | if (endsWith(output, ".gz"))
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:139:9: error: ‘endsWith’ was not declared in this scope; did you mean ‘seqan2::endsWith’?
139 | if (endsWith(output, ".gz"))
| ^~~~~~~~
| seqan2::endsWith
In file included from /usr/include/seqan/sequence.h:99:
/usr/include/seqan/sequence/segment_utils.h:90:13: note: ‘seqan2::endsWith’ declared here
90 | inline bool endsWith(TLhs const & lhs, TRhs const & rhs)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:140:33: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
140 | output = prefix(output, length(output) - 3);
| ^~~~~~
| seqan2::length
In file included from /usr/include/seqan/seeds.h:78:
/usr/include/seqan/seeds/seeds_seed_set_unordered.h:177:1: note: ‘seqan2::length’ declared here
177 | length(SeedSet<TSeed, Unordered> const & seedSet)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:140:18: error: ‘prefix’ was not declared in this scope; did you mean ‘seqan2::prefix’?
140 | output = prefix(output, length(output) - 3);
| ^~~~~~
| seqan2::prefix
In file included from /usr/include/seqan/index/index_pizzachili.h:39,
from /usr/include/seqan/index.h:194:
/usr/include/seqan/index/index_pizzachili_string.h:719:1: note: ‘seqan2::prefix’ declared here
719 | prefix(
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:142:33: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
142 | output = prefix(output, length(output) - 4);
| ^~~~~~
| seqan2::length
/usr/include/seqan/seeds/seeds_seed_set_unordered.h:177:1: note: ‘seqan2::length’ declared here
177 | length(SeedSet<TSeed, Unordered> const & seedSet)
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:142:18: error: ‘prefix’ was not declared in this scope; did you mean ‘seqan2::prefix’?
142 | output = prefix(output, length(output) - 4);
| ^~~~~~
| seqan2::prefix
/usr/include/seqan/index/index_pizzachili_string.h:719:1: note: ‘seqan2::prefix’ declared here
719 | prefix(
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:144:18: error: ‘output’ was not declared in this scope
144 | if (endsWith(output, ".m0"))
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:144:9: error: ‘endsWith’ was not declared in this scope; did you mean ‘seqan2::endsWith’?
144 | if (endsWith(output, ".m0"))
| ^~~~~~~~
| seqan2::endsWith
/usr/include/seqan/sequence/segment_utils.h:90:13: note: ‘seqan2::endsWith’ declared here
90 | inline bool endsWith(TLhs const & lhs, TRhs const & rhs)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:145:34: error: ‘BlastReport’ was not declared in this scope; did you mean ‘seqan2::BlastReport’?
145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^~~~~~~~~~~
| seqan2::BlastReport
/usr/include/seqan/blast/blast_report_out.h:78:27: note: ‘seqan2::BlastReport’ declared here
78 | typedef Tag<BlastReport_> BlastReport;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:145:49: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:145:74: error: ‘BlastTabularSpec’ has not been declared
145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:145:105: error: expected primary-expression before ‘)’ token
145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:147:34: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’?
147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^~~~~~~~~~~~
| seqan2::BlastTabular
/usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here
86 | typedef Tag<BlastTabular_> BlastTabular;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:147:50: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:147:75: error: ‘BlastTabularSpec’ has not been declared
147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:147:106: error: expected primary-expression before ‘)’ token
147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:149:34: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’?
149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^~~~~~~~~~~~
| seqan2::BlastTabular
/usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here
86 | typedef Tag<BlastTabular_> BlastTabular;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:149:50: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:149:75: error: ‘BlastTabularSpec’ has not been declared
149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:149:103: error: expected primary-expression before ‘)’ token
149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:151:34: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’?
151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^~~~~~~~~~~~
| seqan2::BlastTabular
/usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here
86 | typedef Tag<BlastTabular_> BlastTabular;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:151:50: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:151:75: error: ‘BlastTabularSpec’ has not been declared
151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:151:103: error: expected primary-expression before ‘)’ token
151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:158:11: error: ‘BlastTabularSpec’ has not been declared
158 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:162:10: error: ‘BlastTabularSpecSelector’ has not been declared
162 | BlastTabularSpecSelector<h> const &)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:162:34: error: expected ‘,’ or ‘...’ before ‘<’ token
162 | BlastTabularSpecSelector<h> const &)
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv1(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:164:20: error: ‘const struct LambdaOptions’ has no member named ‘blastProgram’
164 | switch(options.blastProgram)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:167:14: error: ‘BlastProgram’ has not been declared
167 | case BlastProgram::BLASTN:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:170:29: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
170 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:170:54: error: ‘h’ was not declared in this scope
170 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:170:57: error: expected primary-expression before ‘)’ token
170 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:171:29: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
171 | BlastProgramSelector<BlastProgram::BLASTN>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:171:50: error: ‘BlastProgram’ has not been declared
171 | BlastProgramSelector<BlastProgram::BLASTN>(),
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:171:72: error: expected primary-expression before ‘)’ token
171 | BlastProgramSelector<BlastProgram::BLASTN>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:172:29: error: there are no arguments to ‘Dna5’ that depend on a template parameter, so a declaration of ‘Dna5’ must be available [-fpermissive]
172 | Dna5());
| ^~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:174:14: error: ‘BlastProgram’ has not been declared
174 | case BlastProgram::BLASTP:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:177:57: error: expected primary-expression before ‘)’ token
177 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:178:50: error: ‘BlastProgram’ has not been declared
178 | BlastProgramSelector<BlastProgram::BLASTP>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:178:72: error: expected primary-expression before ‘)’ token
178 | BlastProgramSelector<BlastProgram::BLASTP>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:179:14: error: ‘BlastProgram’ has not been declared
179 | case BlastProgram::BLASTX:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:182:57: error: expected primary-expression before ‘)’ token
182 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:183:50: error: ‘BlastProgram’ has not been declared
183 | BlastProgramSelector<BlastProgram::BLASTX>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:183:72: error: expected primary-expression before ‘)’ token
183 | BlastProgramSelector<BlastProgram::BLASTX>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:185:14: error: ‘BlastProgram’ has not been declared
185 | case BlastProgram::TBLASTN:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:188:57: error: expected primary-expression before ‘)’ token
188 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:189:50: error: ‘BlastProgram’ has not been declared
189 | BlastProgramSelector<BlastProgram::TBLASTN>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:189:73: error: expected primary-expression before ‘)’ token
189 | BlastProgramSelector<BlastProgram::TBLASTN>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:190:14: error: ‘BlastProgram’ has not been declared
190 | case BlastProgram::TBLASTX:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:193:57: error: expected primary-expression before ‘)’ token
193 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:194:50: error: ‘BlastProgram’ has not been declared
194 | BlastProgramSelector<BlastProgram::TBLASTX>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:194:73: error: expected primary-expression before ‘)’ token
194 | BlastProgramSelector<BlastProgram::TBLASTX>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:206:11: error: ‘BlastTabularSpec’ has not been declared
206 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:207:11: error: ‘BlastProgram’ has not been declared
207 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:211:10: error: ‘BlastTabularSpecSelector’ has not been declared
211 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:211:34: error: expected ‘,’ or ‘...’ before ‘<’ token
211 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv2(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:214:16: error: ‘BlastTabularSpecSelector’ does not name a type
214 | using Th = BlastTabularSpecSelector<h>;
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:215:16: error: ‘BlastProgramSelector’ does not name a type
215 | using Tp = BlastProgramSelector<p>;
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:219:52: error: there are no arguments to ‘Th’ that depend on a template parameter, so a declaration of ‘Th’ must be available [-fpermissive]
219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:219:58: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-fpermissive]
219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:219:64: error: there are no arguments to ‘AminoAcid’ that depend on a template parameter, so a declaration of ‘AminoAcid’ must be available [-fpermissive]
219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:52: error: there are no arguments to ‘Th’ that depend on a template parameter, so a declaration of ‘Th’ must be available [-fpermissive]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:58: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-fpermissive]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:64: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’?
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:81: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’?
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~~~~~~~
| seqan2::Murphy10
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here
85 | typedef Tag<Murphy10_> Murphy10;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:91: error: expected primary-expression before ‘)’ token
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:242:11: error: ‘BlastTabularSpec’ has not been declared
242 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:243:11: error: ‘BlastProgram’ has not been declared
243 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:247:10: error: ‘BlastTabularSpecSelector’ has not been declared
247 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:247:34: error: expected ‘,’ or ‘...’ before ‘<’ token
247 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv3(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:268:25: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
268 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:268:50: error: ‘h’ was not declared in this scope
268 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:268:53: error: expected primary-expression before ‘)’ token
268 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:269:25: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
269 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:269:46: error: ‘p’ was not declared in this scope
269 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:269:49: error: expected primary-expression before ‘)’ token
269 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:271:25: error: there are no arguments to ‘AffineGaps’ that depend on a template parameter, so a declaration of ‘AffineGaps’ must be available [-fpermissive]
271 | AffineGaps());
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:277:11: error: ‘BlastTabularSpec’ has not been declared
277 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:278:11: error: ‘BlastProgram’ has not been declared
278 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:282:10: error: ‘BlastTabularSpecSelector’ has not been declared
282 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:282:34: error: expected ‘,’ or ‘...’ before ‘<’ token
282 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv4(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:316:25: error: ‘IndexSa’ was not declared in this scope; did you mean ‘seqan2::IndexSa’?
316 | return realMain<IndexSa<>>(options,
| ^~~~~~~
| seqan2::IndexSa
In file included from /usr/include/seqan/index.h:142:
/usr/include/seqan/index/index_sa_stree.h:58:8: note: ‘seqan2::IndexSa’ declared here
58 | struct IndexSa {};
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:316:16: error: parse error in template argument list
316 | return realMain<IndexSa<>>(options,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:318:36: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
318 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:318:61: error: ‘h’ was not declared in this scope
318 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:318:64: error: expected primary-expression before ‘)’ token
318 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:319:36: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
319 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:319:57: error: ‘p’ was not declared in this scope
319 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:319:60: error: expected primary-expression before ‘)’ token
319 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:323:25: error: ‘TFMIndex’ was not declared in this scope
323 | return realMain<TFMIndex<>>(options,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:323:16: error: parse error in template argument list
323 | return realMain<TFMIndex<>>(options,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:325:36: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’?
325 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:325:61: error: ‘h’ was not declared in this scope
325 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:325:64: error: expected primary-expression before ‘)’ token
325 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:326:36: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’?
326 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:326:57: error: ‘p’ was not declared in this scope
326 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:326:60: error: expected primary-expression before ‘)’ token
326 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:341:11: error: ‘BlastProgram’ has not been declared
341 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:342:11: error: ‘BlastTabularSpec’ has not been declared
342 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:346:10: error: ‘BlastTabularSpecSelector’ has not been declared
346 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:346:34: error: expected ‘,’ or ‘...’ before ‘<’ token
346 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int realMain(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:351:78: error: ‘p’ was not declared in this scope
351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:351:81: error: ‘h’ was not declared in this scope
351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:351:82: error: template argument 4 is invalid
351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:351:82: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/src/lambda.cpp:352:42: error: ‘TGlobalHolder’ was not declared in this scope; did you mean ‘GlobalDataHolder’?
352 | using TLocalHolder = LocalDataHolder<TGlobalHolder, TScoreExtension>;
| ^~~~~~~~~~~~~
| GlobalDataHolder
/<<PKGBUILDDIR>>/src/lambda.cpp:352:72: error: template argument 1 is invalid
352 | using TLocalHolder = LocalDataHolder<TGlobalHolder, TScoreExtension>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:359:22: error: ‘TLocalHolder’ was not declared in this scope; did you mean ‘totalorder’?
359 | printOptions<TLocalHolder>(options);
| ^~~~~~~~~~~~
| totalorder
/<<PKGBUILDDIR>>/src/lambda.cpp:361:18: error: expected ‘;’ before ‘globalHolder’
361 | TGlobalHolder globalHolder;
| ^~~~~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/lambda.cpp:364:30: error: ‘globalHolder’ was not declared in this scope; did you mean ‘GlobalDataHolder’?
364 | int ret = prepareScoring(globalHolder, options);
| ^~~~~~~~~~~~
| GlobalDataHolder
/<<PKGBUILDDIR>>/src/lambda.cpp:421:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
421 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:428:27: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-fpermissive]
428 | : length(globalHolder.qryIds));
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:434:9: error: ‘TLocalHolder’ was not declared in this scope; did you mean ‘totalorder’?
434 | TLocalHolder localHolder(options, globalHolder);
| ^~~~~~~~~~~~
| totalorder
/<<PKGBUILDDIR>>/src/lambda.cpp:441:13: error: ‘localHolder’ was not declared in this scope
441 | localHolder.init(t);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:481:35: error: ‘localHolder’ was not declared in this scope
481 | globalHolder.stats += localHolder.stats;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:492:42: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-fpermissive]
492 | myPrint(options, 2, "Runtime: ", sysTime() - start, "s.\n\n");
| ^~~~~~~
make[3]: *** [src/CMakeFiles/lambda_indexer.dir/build.make:82: src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[2]: *** [CMakeFiles/Makefile2:193: src/CMakeFiles/lambda_indexer.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: *** [src/CMakeFiles/lambda.dir/build.make:82: src/CMakeFiles/lambda.dir/lambda.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[2]: *** [CMakeFiles/Makefile2:162: src/CMakeFiles/lambda.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build'
dh_auto_build: error: cd build && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:7: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-23T10:29:04Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: arm64
Build Type: binary
Build-Space: 2412
Build-Time: 13
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 24
Job: /tmp/debusine-fetch-exec-upload-xsvahb1s/lambda-align_1.0.3-6.dsc
Machine Architecture: arm64
Package: lambda-align
Package-Time: 67
Source-Version: 1.0.3-6
Space: 2412
Status: attempted
Version: 1.0.3-6
--------------------------------------------------------------------------------
Finished at 2024-11-23T10:29:04Z
Build needed 00:01:07, 2412k disk space