sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-02.freexian.com
+==============================================================================+
| pizzly 0.37.3+ds-9 (arm64) Sat, 23 Nov 2024 10:27:58 +0000 |
+==============================================================================+
Package: pizzly
Version: 0.37.3+ds-9
Source Version: 0.37.3+ds-9
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.GsgEQNDBXh...
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'.
Finished processing commands.
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Copying /tmp/debusine-fetch-exec-upload-e8a3d_91/seqan-apps-dbgsym_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-e8a3d_91/seqan-apps_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-e8a3d_91/libseqan2-dev_2.5.0~rc3+dfsg-1_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/pizzly-gAbhUg/resolver-xUwKej' with '<<RESOLVERDIR>>'
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| Update chroot |
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Get:1 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ InRelease
Ign:1 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ InRelease
Get:2 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ Release [606 B]
Get:2 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ Release [606 B]
Get:3 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ Release.gpg
Ign:3 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ Release.gpg
Get:4 http://deb.debian.org/debian sid InRelease [202 kB]
Get:5 file:/build/pizzly-gAbhUg/resolver-ibBufu/apt_archive ./ Packages [4687 B]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9958 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4913 kB]
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
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.
Need to get 2411 kB of archives.
After this operation, 206 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 base-files arm64 13.6 [72.9 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.14 [969 kB]
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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Preparing to unpack .../libxml-sax-perl_1.02+dfsg-4_all.deb ...
Unpacking libxml-sax-perl (1.02+dfsg-4) over (1.02+dfsg-3) ...
Setting up libxml-sax-perl (1.02+dfsg-4) ...
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...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-3) ...
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| Fetch source files |
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Local sources
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/tmp/debusine-fetch-exec-upload-e8a3d_91/pizzly_0.37.3+ds-9.dsc exists in /tmp/debusine-fetch-exec-upload-e8a3d_91; copying to chroot
I: NOTICE: Log filtering will replace 'build/pizzly-gAbhUg/pizzly-0.37.3+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pizzly-gAbhUg' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libseqan2-dev, help2man, cmake, kallisto, zlib1g-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libseqan2-dev, help2man, cmake, kallisto, zlib1g-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Ign:3 file:/<<BUILDDIR>>/resolver-ibBufu/apt_archive ./ Release.gpg
Reading package lists...
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Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
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 help2man kallisto
libarchive13t64 libasan8 libc-dev-bin libc6-dev libcc1-0 libcrypt-dev
libcurl4t64 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot
libfile-stripnondeterminism-perl libgcc-14-dev libhts3t64 libhtscodecs2
libhwasan0 libisl23 libitm1 libjsoncpp26 liblocale-gettext-perl 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:
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 help2man kallisto
libarchive13t64 libasan8 libc-dev-bin libc6-dev libcc1-0 libcrypt-dev
libcurl4t64 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot
libfile-stripnondeterminism-perl libgcc-14-dev libhts3t64 libhtscodecs2
libhwasan0 libisl23 libitm1 libjsoncpp26 liblocale-gettext-perl 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, 66 newly installed, 0 to remove and 0 not upgraded.
Need to get 77.2 MB/78.4 MB of archives.
After this operation, 311 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-ibBufu/apt_archive ./ libseqan2-dev 2.5.0~rc3+dfsg-1 [1222 kB]
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Get:3 http://deb.debian.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB]
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Get:41 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:42 http://deb.debian.org/debian sid/main arm64 cmake-data all 3.31.1-1 [2267 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB]
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Get:47 http://deb.debian.org/debian sid/main arm64 librhash1 arm64 1.4.5-1 [129 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 cmake arm64 3.31.1-1 [9873 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:55 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 help2man arm64 1.49.3+b1 [198 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 kallisto arm64 0.48.0+dfsg-4+b2 [256 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
debconf: delaying package configuration, since apt-utils is not installed
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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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mawk_1.3.4.20240905-1 mount_2.40.2-11 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 openssl_3.3.2-2 openssl-provider-legacy_3.3.2-2 passwd_1:4.16.0-5 patch_2.7.6-7+b1 patchutils_0.4.2-1+b1 perl_5.40.0-7 perl-base_5.40.0-7 perl-modules-5.40_5.40.0-7 perl-openssl-defaults_7+b2 plzip_1.11-2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 readline-common_8.2-5 rpcsvc-proto_1.4.3-1+b1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2+b1 sensible-utils_0.0.24 shared-mime-info_2.4-5+b1 sysvinit-utils_3.11-1 t1utils_1.41-4+b1 tar_1.35+dfsg-3+b1 tzdata_2024b-3 ucf_3.0043+nmu1 unzip_6.0-28+b1 util-linux_2.40.2-11 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
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Format: 3.0 (quilt)
Source: pizzly
Binary: pizzly
Architecture: any
Version: 0.37.3+ds-9
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: https://github.com/pmelsted/pizzly
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/pizzly
Vcs-Git: https://salsa.debian.org/med-team/pizzly.git
Testsuite: autopkgtest
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gpgv: Signature made Thu Jan 26 08:37:46 2023 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pizzly_0.37.3+ds-9.dsc: no acceptable signature found
dpkg-source: info: extracting pizzly in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pizzly_0.37.3+ds.orig.tar.xz
dpkg-source: info: unpacking pizzly_0.37.3+ds-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying executable-not-elf-or-script.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 pizzly
dpkg-buildpackage: info: source version 0.37.3+ds-9
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -f debian/pizzly.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/pizzly.substvars debian/files
rm -fr -- debian/pizzly/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-aarch64-linux-gnu && 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 -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ..
CMake Deprecation Warning at CMakeLists.txt:2 (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.
-- 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
-- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Configuring done (1.0s)
-- 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>>/obj-aarch64-linux-gnu
dh_auto_build
cd obj-aarch64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f CMakeFiles/pizzly.dir/build.make CMakeFiles/pizzly.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles/pizzly.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f CMakeFiles/pizzly.dir/build.make CMakeFiles/pizzly.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 50%] Building CXX object CMakeFiles/pizzly.dir/main.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/. -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/pizzly.dir/main.cpp.o -MF CMakeFiles/pizzly.dir/main.cpp.o.d -o CMakeFiles/pizzly.dir/main.cpp.o -c /<<PKGBUILDDIR>>/main.cpp
In file included from /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /usr/include/seqan/seq_io/bam_sam.h:39,
from /usr/include/seqan/seq_io.h:55,
from /<<PKGBUILDDIR>>/main.cpp:3:
/usr/include/seqan/align/dp_matrix_navigator_score_matrix.h:364:31: error: ‘is_same_v’ is not a member of ‘std’; did you mean ‘is_same’?
364 | inline std::enable_if_t<!std::is_same_v<TColumnType, DPInitialColumn>>
| ^~~~~~~~~
| is_same
/usr/include/seqan/align/dp_matrix_navigator_score_matrix.h:364:54: error: template argument 1 is invalid
364 | inline std::enable_if_t<!std::is_same_v<TColumnType, DPInitialColumn>>
| ^~~~~~~~~~~~~~~
/usr/include/seqan/align/dp_matrix_navigator_score_matrix.h:364:69: error: expected unqualified-id before ‘>’ token
364 | inline std::enable_if_t<!std::is_same_v<TColumnType, DPInitialColumn>>
| ^~
/usr/include/seqan/align/dp_matrix_navigator_score_matrix.h:375:31: error: ‘is_same_v’ is not a member of ‘std’; did you mean ‘is_same’?
375 | inline std::enable_if_t<!std::is_same_v<TColumnType, DPInitialColumn>>
| ^~~~~~~~~
| is_same
/usr/include/seqan/align/dp_matrix_navigator_score_matrix.h:375:54: error: template argument 1 is invalid
375 | inline std::enable_if_t<!std::is_same_v<TColumnType, DPInitialColumn>>
| ^~~~~~~~~~~~~~~
/usr/include/seqan/align/dp_matrix_navigator_score_matrix.h:375:69: error: expected unqualified-id before ‘>’ token
375 | inline std::enable_if_t<!std::is_same_v<TColumnType, DPInitialColumn>>
| ^~
In file included from /<<PKGBUILDDIR>>/main.cpp:6:
/<<PKGBUILDDIR>>/common.h: In constructor ‘ProgramOptions::ProgramOptions()’:
/<<PKGBUILDDIR>>/common.h:18:7: warning: ‘ProgramOptions::kmerScore’ will be initialized after [-Wreorder]
18 | int kmerScore;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/common.h:17:7: warning: ‘int ProgramOptions::insertSize’ [-Wreorder]
17 | int insertSize;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/common.h:19:3: warning: when initialized here [-Wreorder]
19 | ProgramOptions() : kmerScore(2), insertSize(400), ignoreProtein(false) {}
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/common.h:17:7: warning: ‘ProgramOptions::insertSize’ will be initialized after [-Wreorder]
17 | int insertSize;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/common.h:14:8: warning: ‘bool ProgramOptions::ignoreProtein’ [-Wreorder]
14 | bool ignoreProtein;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/common.h:19:3: warning: when initialized here [-Wreorder]
19 | ProgramOptions() : kmerScore(2), insertSize(400), ignoreProtein(false) {}
| ^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/main.cpp:8:
/<<PKGBUILDDIR>>/GeneModel.hpp: At global scope:
/<<PKGBUILDDIR>>/GeneModel.hpp:92:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
92 | std::unordered_map<std::string, seqan::CharString> seqs;
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:92:52: error: template argument 2 is invalid
92 | std::unordered_map<std::string, seqan::CharString> seqs;
| ^
/<<PKGBUILDDIR>>/GeneModel.hpp:92:52: error: template argument 5 is invalid
/<<PKGBUILDDIR>>/GeneModel.hpp: In member function ‘bool Transcriptome::translateTrPosition(const std::string&, int, std::string&, int&, std::string&)’:
/<<PKGBUILDDIR>>/GeneModel.hpp:117:10: warning: unused variable ‘fw’ [-Wunused-variable]
117 | bool fw = (trxmodel.strand == Strandedness::FORWARD);
| ^~
/<<PKGBUILDDIR>>/GeneModel.hpp: In function ‘void writeTranscriptome(Transcriptome&, std::ostream&)’:
/<<PKGBUILDDIR>>/GeneModel.hpp:146:17: warning: unused variable ‘gene_id’ [-Wunused-variable]
146 | const auto &gene_id = gene.first;
| ^~~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:172:19: warning: unused variable ‘tr_id’ [-Wunused-variable]
172 | const auto &tr_id = trlist.first;
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp: In function ‘void parseFasta(Transcriptome&, const std::string&)’:
/<<PKGBUILDDIR>>/GeneModel.hpp:257:3: error: ‘seqan’ has not been declared
257 | seqan::SeqFileIn seqFileIn(seqan::toCString(fasta_fn));
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:258:3: error: ‘seqan’ has not been declared
258 | seqan::CharString id;
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:259:3: error: ‘seqan’ has not been declared
259 | seqan::CharString seq;
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:261:16: error: ‘seqFileIn’ was not declared in this scope
261 | while(!atEnd(seqFileIn)) {
| ^~~~~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:261:10: error: ‘atEnd’ was not declared in this scope; did you mean ‘seqan2::atEnd’?
261 | while(!atEnd(seqFileIn)) {
| ^~~~~
| seqan2::atEnd
In file included from /usr/include/seqan/store.h:61,
from /usr/include/seqan/seq_io/fai_index.h:41,
from /usr/include/seqan/seq_io.h:73:
/usr/include/seqan/store/store_annotation.h:623:1: note: ‘seqan2::atEnd’ declared here
623 | atEnd(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:262:5: error: ‘seqan’ has not been declared
262 | seqan::readRecord(id,seq,seqFileIn);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:262:23: error: ‘id’ was not declared in this scope
262 | seqan::readRecord(id,seq,seqFileIn);
| ^~
/<<PKGBUILDDIR>>/GeneModel.hpp:262:26: error: ‘seq’ was not declared in this scope
262 | seqan::readRecord(id,seq,seqFileIn);
| ^~~
/<<PKGBUILDDIR>>/GeneModel.hpp:263:36: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
263 | std::string name = std::string(seqan::toCString(id));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:266:5: error: ‘seqan’ is not a class, namespace, or enumeration
266 | seqan::toUpper(seq);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:267:24: error: request for member ‘insert’ in ‘transcriptome.Transcriptome::seqs’, which is of non-class type ‘int’
267 | transcriptome.seqs.insert({name.substr(0,std::min(sp,pipe)), std::move(seq)});
| ^~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp: In function ‘void parseGTF(Transcriptome&, const std::string&, const ProgramOptions&)’:
/<<PKGBUILDDIR>>/GeneModel.hpp:272:3: error: ‘seqan’ has not been declared
272 | seqan::GffFileIn gtf(gtf_fn.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:273:3: error: ‘seqan’ has not been declared
273 | seqan::GffRecord record;
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:276:10: error: ‘seqan’ has not been declared
276 | while(!seqan::atEnd(gtf)) {
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:276:23: error: ‘gtf’ was not declared in this scope
276 | while(!seqan::atEnd(gtf)) {
| ^~~
/<<PKGBUILDDIR>>/GeneModel.hpp:278:5: error: ‘seqan’ has not been declared
278 | seqan::readRecord(record,gtf);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:278:23: error: ‘record’ was not declared in this scope
278 | seqan::readRecord(record,gtf);
| ^~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:282:27: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
282 | for (int i = 0; i < length(record.tagNames); i++) {
| ^~~~~~
| seqan2::length
In file included from /usr/include/seqan/bam_io.h:62:
/usr/include/seqan/bam_io/bam_tags_dict.h:364:1: note: ‘seqan2::length’ declared here
364 | length(BamTagsDict const & tags)
| ^~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:284:22: error: ‘seqan’ has not been declared
284 | model.id = seqan::toCString(record.tagValues[i]);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:287:24: error: ‘seqan’ has not been declared
287 | model.name = seqan::toCString(record.tagValues[i]);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:290:41: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
290 | std::string val = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:301:38: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
301 | gene_version = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:313:19: error: ‘seqan’ has not been declared
313 | model.chr = seqan::toCString(record.ref);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:329:27: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
329 | for (int i = 0; i < length(record.tagNames); i++) {
| ^~~~~~
| seqan2::length
/usr/include/seqan/bam_io/bam_tags_dict.h:364:1: note: ‘seqan2::length’ declared here
364 | length(BamTagsDict const & tags)
| ^~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:331:21: error: ‘seqan’ has not been declared
331 | gene_id = seqan::toCString(record.tagValues[i]);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:333:22: error: ‘seqan’ has not been declared
333 | model.id = seqan::toCString(record.tagValues[i]);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:336:41: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
336 | std::string val = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:346:38: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
346 | gene_version = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:349:37: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
349 | txp_version = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:359:30: error: ‘seqan’ has not been declared
359 | std::string source = seqan::toCString(record.source);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:371:19: error: ‘seqan’ has not been declared
371 | model.chr = seqan::toCString(record.ref);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:392:27: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
392 | for (int i = 0; i < length(record.tagNames); i++) {
| ^~~~~~
| seqan2::length
/usr/include/seqan/bam_io/bam_tags_dict.h:364:1: note: ‘seqan2::length’ declared here
364 | length(BamTagsDict const & tags)
| ^~~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:394:21: error: ‘seqan’ has not been declared
394 | gene_id = seqan::toCString(record.tagValues[i]);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:396:20: error: ‘seqan’ has not been declared
396 | trx_id = seqan::toCString(record.tagValues[i]);
| ^~~~~
/<<PKGBUILDDIR>>/GeneModel.hpp:399:38: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
399 | gene_version = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:402:37: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
402 | txp_version = std::string(seqan::toCString(record.tagValues[i]));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/GeneModel.hpp:411:19: error: ‘seqan’ has not been declared
411 | model.chr = seqan::toCString(record.ref);
| ^~~~~
In file included from /<<PKGBUILDDIR>>/main.cpp:9:
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:205:27: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
205 | return std::move(m);
| ~~~~~~~~~^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:205:27: note: remove ‘std::move’ call
/<<PKGBUILDDIR>>/FilterFusions.hpp:214:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
214 | return std::move(m);
| ~~~~~~~~~^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:214:21: note: remove ‘std::move’ call
/<<PKGBUILDDIR>>/FilterFusions.hpp: In function ‘bool filterFusionRecord(const Transcriptome&, ProgramOptions&, const FusionRecord&, SplitRecord&)’:
/<<PKGBUILDDIR>>/FilterFusions.hpp:233:11: error: ‘seqan’ does not name a type
233 | typedef seqan::CharString TSeq;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:234:3: error: ‘TSeq’ was not declared in this scope
234 | TSeq rs1(rec.seq1.substr(rec.kpos1.first, options.k + rec.kpos1.second-rec.kpos1.first).c_str());
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:235:7: error: expected ‘;’ before ‘rs2’
235 | TSeq rs2(rec.seq2.substr(rec.kpos2.first, options.k + rec.kpos2.second-rec.kpos2.first).c_str());
| ^~~~
| ;
/<<PKGBUILDDIR>>/FilterFusions.hpp:238:3: error: ‘seqan’ has not been declared
238 | seqan::Align<TSeq, seqan::ArrayGaps> align;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:238:22: error: ‘seqan’ has not been declared
238 | seqan::Align<TSeq, seqan::ArrayGaps> align;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:238:40: error: ‘align’ was not declared in this scope
238 | seqan::Align<TSeq, seqan::ArrayGaps> align;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:238:40: note: suggested alternatives:
In file included from /usr/include/c++/14/memory:74,
from /usr/include/seqan/basic/test_system.h:53,
from /usr/include/seqan/basic.h:65,
from /usr/include/seqan/arg_parse.h:44,
from /<<PKGBUILDDIR>>/main.cpp:2:
/usr/include/c++/14/bits/align.h:61:1: note: ‘std::align’
61 | align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept
| ^~~~~
In file included from /usr/include/seqan/index.h:224,
from /<<PKGBUILDDIR>>/FilterFusions.hpp:17:
/usr/include/seqan/index/find_backtracking.h:358:13: note: ‘seqan2::align’
358 | inline bool align(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:239:3: error: ‘seqan’ has not been declared
239 | seqan::resize(rows(align), 2);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:239:17: error: ‘rows’ was not declared in this scope; did you mean ‘seqan2::rows’?
239 | seqan::resize(rows(align), 2);
| ^~~~
| seqan2::rows
In file included from /usr/include/seqan/align.h:97:
/usr/include/seqan/align/align_base.h:341:1: note: ‘seqan2::rows’ declared here
341 | rows(Align<TSource, TSpec> const & me)
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:241:33: error: ‘TSeq’ is not a type
241 | auto mapKmersWithErrors = [&](TSeq& krseq, const std::vector<TranscriptPos> &trlist) -> bool {
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:242:13: error: ‘seqan’ does not name a type
242 | typedef seqan::Index<seqan::StringSet<TSeq>, seqan::IndexQGram<seqan::Shape<seqan::Dna, seqan::UngappedShape<8> >, seqan::OpenAddressing> > TIndex;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:243:13: error: ‘seqan’ does not name a type
243 | typedef seqan::Pattern<TIndex, seqan::Swift<seqan::SwiftSemiGlobal> > TPattern;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:244:13: error: ‘seqan’ does not name a type
244 | typedef seqan::Finder<const TSeq, seqan::Swift<seqan::SwiftSemiGlobal> > TFinder;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:245:5: error: ‘seqan’ has not been declared
245 | seqan::StringSet<TSeq> reads;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:245:28: error: ‘reads’ was not declared in this scope; did you mean ‘read’?
245 | seqan::StringSet<TSeq> reads;
| ^~~~~
| read
/<<PKGBUILDDIR>>/FilterFusions.hpp:246:5: error: ‘appendValue’ was not declared in this scope; did you mean ‘seqan2::appendValue’?
246 | appendValue(reads,krseq);
| ^~~~~~~~~~~
| seqan2::appendValue
In file included from /usr/include/seqan/index.h:153:
/usr/include/seqan/index/index_fm_rank_dictionary_levels.h:1623:13: note: ‘seqan2::appendValue’ declared here
1623 | inline void appendValue(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TChar const c, Tag<TExpand> const tag)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:247:5: error: ‘seqan’ has not been declared
247 | seqan::reverseComplement(krseq);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:249:5: error: ‘TIndex’ was not declared in this scope; did you mean ‘rindex’?
249 | TIndex index(reads);
| ^~~~~~
| rindex
/<<PKGBUILDDIR>>/FilterFusions.hpp:250:5: error: ‘TPattern’ was not declared in this scope
250 | TPattern pattern(index);
| ^~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:251:20: error: ‘seqan’ has not been declared
251 | int matchlen = seqan::length(krseq);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:256:33: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
256 | const auto &it = trx.seqs.find(tr.tr);
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:257:26: error: request for member ‘end’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
257 | if (it != trx.seqs.end()) {
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:258:15: error: ‘TSeq’ does not name a type
258 | const TSeq &trseq = it->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:259:9: error: ‘TFinder’ was not declared in this scope
259 | TFinder finder(trseq);
| ^~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:260:21: error: ‘finder’ was not declared in this scope; did you mean ‘rindex’?
260 | while (find(finder, pattern, epsilon, options.k)) {
| ^~~~~~
| rindex
/<<PKGBUILDDIR>>/FilterFusions.hpp:260:29: error: ‘pattern’ was not declared in this scope
260 | while (find(finder, pattern, epsilon, options.k)) {
| ^~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:260:16: error: ‘find’ was not declared in this scope
260 | while (find(finder, pattern, epsilon, options.k)) {
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:260:16: note: suggested alternatives:
In file included from /usr/include/c++/14/algorithm:61,
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/bits/stl_algo.h:3841:5: note: ‘std::find’
3841 | find(_InputIterator __first, _InputIterator __last,
| ^~~~
In file included from /usr/include/seqan/index.h:242:
/usr/include/seqan/index/find_index_lambda.h:254:1: note: ‘seqan2::find’
254 | find(TIndex & index,
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:261:11: error: ‘seqan’ has not been declared
261 | seqan::Finder<const TSeq> verifyFinder(trseq);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:261:25: error: expected primary-expression before ‘const’
261 | seqan::Finder<const TSeq> verifyFinder(trseq);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:262:11: error: ‘seqan’ has not been declared
262 | seqan::setPosition(verifyFinder, seqan::beginPosition(finder));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:262:30: error: ‘verifyFinder’ was not declared in this scope
262 | seqan::setPosition(verifyFinder, seqan::beginPosition(finder));
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:262:44: error: ‘seqan’ has not been declared
262 | seqan::setPosition(verifyFinder, seqan::beginPosition(finder));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:263:11: error: ‘seqan’ has not been declared
263 | seqan::Pattern<const TSeq, seqan::Myers<>> verifyPattern(reads[seqan::position(pattern).i1]);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:263:26: error: expected primary-expression before ‘const’
263 | seqan::Pattern<const TSeq, seqan::Myers<>> verifyPattern(reads[seqan::position(pattern).i1]);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:264:18: error: ‘seqan’ has not been declared
264 | while (seqan::find(verifyFinder, verifyPattern, -((int) (epsilon*options.k)))
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:264:44: error: ‘verifyPattern’ was not declared in this scope
264 | while (seqan::find(verifyFinder, verifyPattern, -((int) (epsilon*options.k)))
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:265:18: error: ‘seqan’ has not been declared
265 | && seqan::position(verifyFinder) < seqan::endPosition(seqan::infix(finder))) {
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:265:50: error: ‘seqan’ has not been declared
265 | && seqan::position(verifyFinder) < seqan::endPosition(seqan::infix(finder))) {
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:265:69: error: ‘seqan’ has not been declared
265 | && seqan::position(verifyFinder) < seqan::endPosition(seqan::infix(finder))) {
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:251:9: warning: unused variable ‘matchlen’ [-Wunused-variable]
251 | int matchlen = seqan::length(krseq);
| ^~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In function ‘bool filterFusionRecord(const Transcriptome&, ProgramOptions&, const FusionRecord&, SplitRecord&)’:
/<<PKGBUILDDIR>>/FilterFusions.hpp:277:26: error: ‘rs1’ was not declared in this scope
277 | if (mapKmersWithErrors(rs1,rec.tr2)) {
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:280:26: error: ‘rs2’ was not declared in this scope
280 | if (mapKmersWithErrors(rs2,rec.tr1)) {
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:301:36: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
301 | const auto& trseq = trx.seqs.find(trmodel.id)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:311:21: error: ‘seqan’ has not been declared
311 | if (tr_stop > seqan::length(trseq)) {
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:312:19: error: ‘seqan’ has not been declared
312 | tr_stop = seqan::length(trseq);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:315:25: error: ‘seqan’ has not been declared
315 | auto read_match = seqan::CharString(seqan::infix(trseq, tr_start, tr_stop));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:315:43: error: ‘seqan’ has not been declared
315 | auto read_match = seqan::CharString(seqan::infix(trseq, tr_start, tr_stop));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:317:9: error: ‘seqan’ has not been declared
317 | seqan::reverseComplement(read_match);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:320:24: error: ‘seqan’ has not been declared
320 | std::string tseq(seqan::toCString(read_match));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:323:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
323 | return std::move(tlist);
| ~~~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:323:21: note: remove ‘std::move’ call
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:335:7: error: ‘seqan’ has not been declared
335 | seqan::CharString read(seq.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:336:7: error: ‘seqan’ has not been declared
336 | seqan::CharString ref(tseq.c_str()); // inefficient, refactor at some point
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:20: error: ‘seqan’ has not been declared
338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:54: error: ‘ref’ was not declared in this scope; did you mean ‘std::ref’?
338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector());
| ^~~
| std::ref
In file included from /usr/include/c++/14/string:52,
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/main.cpp:1:
/usr/include/c++/14/bits/refwrap.h:445:5: note: ‘std::ref’ declared here
445 | ref(reference_wrapper<_Tp> __t) noexcept
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:59: error: ‘seqan’ has not been declared
338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:332:13: warning: unused variable ‘tseq’ [-Wunused-variable]
332 | auto& tseq = it.first;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:403:9: error: ‘seqan’ has not been declared
403 | seqan::CharString read(seq.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:404:9: error: ‘seqan’ has not been declared
404 | seqan::CharString splitref(tsplit.first.c_str()); // inefficient, refactor at some point
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:405:9: error: ‘seqan’ has not been declared
405 | seqan::CharString saferef(tsafe.first.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:9: error: ‘seqan’ has not been declared
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:21: error: ‘seqan’ has not been declared
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:40: error: ‘readRowLeft’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:53: error: ‘readRowRight’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:67: error: ‘splitRowLeft’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:81: error: ‘safeRowRight’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:408:9: error: ‘seqan’ has not been declared
408 | seqan::setSource(readRowLeft, read);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:409:9: error: ‘seqan’ has not been declared
409 | seqan::setSource(readRowRight, read);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:410:9: error: ‘seqan’ has not been declared
410 | seqan::setSource(splitRowLeft, splitref);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:410:40: error: ‘splitref’ was not declared in this scope; did you mean ‘splitrec’?
410 | seqan::setSource(splitRowLeft, splitref);
| ^~~~~~~~
| splitrec
/<<PKGBUILDDIR>>/FilterFusions.hpp:411:9: error: ‘seqan’ has not been declared
411 | seqan::setSource(safeRowRight, saferef);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:411:40: error: ‘saferef’ was not declared in this scope
411 | seqan::setSource(safeRowRight, saferef);
| ^~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:413:9: error: ‘seqan’ has not been declared
413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:413:22: error: expected primary-expression before ‘int’
413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1);
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:414:9: error: ‘seqan’ has not been declared
414 | seqan::AlignConfig<false, true, true, false> config;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:414:54: error: ‘config’ was not declared in this scope
414 | seqan::AlignConfig<false, true, true, false> config;
| ^~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:415:26: error: ‘seqan’ has not been declared
415 | int splitScore = seqan::splitAlignment(readRowLeft, splitRowLeft, readRowRight, safeRowRight, scoringScheme, config);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:415:103: error: ‘scoringScheme’ was not declared in this scope; did you mean ‘seqan2::scoringScheme’?
415 | int splitScore = seqan::splitAlignment(readRowLeft, splitRowLeft, readRowRight, safeRowRight, scoringScheme, config);
| ^~~~~~~~~~~~~
| seqan2::scoringScheme
In file included from /usr/include/seqan/find.h:93,
from /usr/include/seqan/index.h:46:
/usr/include/seqan/find/find_score.h:180:1: note: ‘seqan2::scoringScheme’ declared here
180 | scoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:426:24: error: ‘seqan’ has not been declared
426 | splitPos = seqan::toSourcePosition(readRowLeft, seqan::clippedEndPosition(readRowLeft));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:426:61: error: ‘seqan’ has not been declared
426 | splitPos = seqan::toSourcePosition(readRowLeft, seqan::clippedEndPosition(readRowLeft));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:433:27: error: ‘seqan’ has not been declared
433 | int t2pos = seqan::toSourcePosition(safeRowRight, 0);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:434:27: error: ‘seqan’ has not been declared
434 | int t2clip= seqan::toSourcePosition(readRowRight, 0); //seqan::clippedBeginPosition(readRowRight));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:436:39: error: ‘seqan’ has not been declared
436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos + (seqan::length(splitref) - t2clip);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:436:73: error: ‘seqan’ has not been declared
436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos + (seqan::length(splitref) - t2clip);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:438:39: error: ‘seqan’ has not been declared
438 | t2copy.pos = t2.pos + seqan::length(saferef) - t2pos -1;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:709:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ExonModel>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
709 | for (int i = 0; i < trm.exons.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:738:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ExonModel>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
738 | for (int i = 0; i < trm.exons.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:765:11: warning: unused variable ‘gap’ [-Wunused-variable]
765 | int gap = d2 - d1;
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:781:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
781 | return std::move(ret);
| ~~~~~~~~~^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:781:21: note: remove ‘std::move’ call
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:872:42: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
872 | const auto & seq1 = trx.seqs.find(sp.tr1)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:873:42: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
873 | const auto & seq2 = trx.seqs.find(sp.tr2)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:883:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
883 | for (int i = 0; i < v.size(); i++) {
| ~~^~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:907:145: error: ‘seqan’ has not been declared
907 | std::string fasta_name = sp.tr1 + "_0:" + std::to_string(tp1) + "_" + sp.tr2 + "_" + std::to_string(tp2) + ":" + std::to_string(seqan::length(seq2));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:920:82: error: ‘seqan’ has not been declared
920 | << ", \"endPos\" : " << std::to_string((sp.dir1) ? tp1 : seqan::length(seq1)) << ", \"edit\" : " << std::to_string(ed1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:924:82: error: ‘seqan’ has not been declared
924 | << ", \"endPos\" : " << std::to_string((sp.dir2) ? tp2 : seqan::length(seq2)) << ", \"edit\" : " << std::to_string(ed2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:929:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
929 | for (int i = 0; i < readsInTr.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:940:29: error: ‘seqan’ has not been declared
940 | << seqan::prefix(seq1, tp1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:941:29: error: ‘seqan’ has not been declared
941 | << seqan::suffix(seq2, tp2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:867:17: warning: unused variable ‘split_reads’ [-Wunused-variable]
867 | int split_reads = spp.second;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:961:33: error: ‘seqan’ has not been declared
961 | int rlen1 = seqan::length(fr.seq1);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:962:33: error: ‘seqan’ has not been declared
962 | int rlen2 = seqan::length(fr.seq2);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:964:50: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
964 | const auto & seq1 = trx.seqs.find(t1.tr)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:965:50: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
965 | const auto & seq2 = trx.seqs.find(t2.tr)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:971:72: error: ‘seqan’ has not been declared
971 | int tp1 = (t1strand) ? std::min(t1.pos+rlen1, (int)seqan::length(seq1)-1) : std::max(t1.pos-rlen1,0);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:972:72: error: ‘seqan’ has not been declared
972 | int tp2 = (t2strand) ? std::min(t2.pos+rlen2, (int)seqan::length(seq2)-1) : std::max(t2.pos-rlen2,0);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1033:29: warning: loop variable ‘p’ creates a copy from type ‘const std::pair<const SplitInfo, std::vector<std::pair<int, int> > >’ [-Wrange-loop-construct]
1033 | for (const auto p : trfmap) {
| ^
/<<PKGBUILDDIR>>/FilterFusions.hpp:1033:29: note: use reference type to prevent copying
1033 | for (const auto p : trfmap) {
| ^
| &
/<<PKGBUILDDIR>>/FilterFusions.hpp:1037:44: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
1037 | const auto & seq1 = trx.seqs.find(spi.tr1)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1038:44: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
1038 | const auto & seq2 = trx.seqs.find(spi.tr2)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1080:145: error: ‘seqan’ has not been declared
1080 | fasta_name = spi.tr1 + "_0:" + std::to_string(spi.pos1) + "_" + spi.tr2 + "_" + std::to_string(spi.pos2) + ":" + std::to_string(seqan::length(seq2));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1083:88: error: ‘seqan’ has not been declared
1083 | << ", \"endPos\" : " << std::to_string((spi.dir1) ? spi.pos1 : seqan::length(seq1))
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1086:88: error: ‘seqan’ has not been declared
1086 | << ", \"endPos\" : " << std::to_string((spi.dir2) ? spi.pos2 : seqan::length(seq2))
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1091:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1091 | for (int i = 0; i < readsInTr.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1102:28: error: ‘seqan’ has not been declared
1102 | << seqan::prefix(seq1, spi.pos1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1103:28: error: ‘seqan’ has not been declared
1103 | << seqan::suffix(seq2, spi.pos2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1115:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1115 | for (int i = 0; i < v.size(); i++) {
| ~~^~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1112:18: warning: unused variable ‘firstJsonRead’ [-Wunused-variable]
1112 | bool firstJsonRead = true;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/main.cpp: At global scope:
/<<PKGBUILDDIR>>/main.cpp:11:1: error: ‘seqan’ does not name a type
11 | seqan::ArgumentParser::ParseResult
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/main.cpp:79:5: error: ‘seqan’ has not been declared
79 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:83:9: error: ‘res’ was not declared in this scope
83 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~
/<<PKGBUILDDIR>>/main.cpp:83:16: error: ‘seqan’ has not been declared
83 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:84:23: error: ‘seqan’ has not been declared
84 | return res == seqan::ArgumentParser::PARSE_ERROR;
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: error: ‘begin’ was not declared in this scope
111 | for (const auto &it : trx.seqs) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: note: suggested alternatives:
In file included from /usr/include/c++/14/string:53:
/usr/include/c++/14/bits/range_access.h:114:37: note: ‘std::begin’
114 | template<typename _Tp> const _Tp* begin(const valarray<_Tp>&) noexcept;
| ^~~~~
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:460:1: note: ‘seqan2::begin’
460 | begin(
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: error: ‘end’ was not declared in this scope
111 | for (const auto &it : trx.seqs) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: note: suggested alternatives:
/usr/include/c++/14/bits/range_access.h:116:37: note: ‘std::end’
116 | template<typename _Tp> const _Tp* end(const valarray<_Tp>&) noexcept;
| ^~~
/usr/include/seqan/index/index_pizzachili_string.h:480:1: note: ‘seqan2::end’
480 | end(
| ^~~
/<<PKGBUILDDIR>>/main.cpp:126:43: error: request for member ‘size’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘int’
126 | } else if (numTxpSeqFound != trx.seqs.size()) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:127:78: error: request for member ‘size’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘int’
127 | std::cerr << "Warning: could not find annotations for " << (trx.seqs.size() - numTxpSeqFound) << " transcripts\n" << std::endl;
| ^~~~
/<<PKGBUILDDIR>>/GeneModel.hpp: In function ‘Strandedness operator~(const Strandedness&)’:
/<<PKGBUILDDIR>>/GeneModel.hpp:18:1: warning: control reaches end of non-void function [-Wreturn-type]
18 | }
| ^
make[3]: *** [CMakeFiles/pizzly.dir/build.make:82: CMakeFiles/pizzly.dir/main.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/pizzly.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[1]: *** [Makefile:94: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-23T10:29:08Z
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: 876
Build-Time: 11
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 28
Job: /tmp/debusine-fetch-exec-upload-e8a3d_91/pizzly_0.37.3+ds-9.dsc
Machine Architecture: arm64
Package: pizzly
Package-Time: 70
Source-Version: 0.37.3+ds-9
Space: 876
Status: attempted
Version: 0.37.3+ds-9
--------------------------------------------------------------------------------
Finished at 2024-11-23T10:29:08Z
Build needed 00:01:10, 876k disk space