sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-07.freexian.com
+==============================================================================+
| hilive 2.0a-4 (arm64) Sat, 23 Nov 2024 10:27:55 +0000 |
+==============================================================================+
Package: hilive
Version: 2.0a-4
Source Version: 2.0a-4
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.LvWKKbbC3w...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Chroot Setup Commands |
+------------------------------------------------------------------------------+
rm -f /etc/resolv.conf
----------------------
I: Finished running 'rm -f /etc/resolv.conf'.
Finished processing commands.
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Copying /tmp/debusine-fetch-exec-upload-cja7d46h/seqan-apps-dbgsym_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-cja7d46h/seqan-apps_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-cja7d46h/libseqan2-dev_2.5.0~rc3+dfsg-1_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/hilive-CGer8W/resolver-YiyRFT' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ InRelease
Ign:1 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ InRelease
Get:2 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ Release [606 B]
Get:2 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ Release [606 B]
Get:3 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ Release.gpg
Ign:3 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ Release.gpg
Get:4 file:/build/hilive-CGer8W/resolver-T6e2uA/apt_archive ./ Packages [4687 B]
Get:5 http://deb.debian.org/debian sid InRelease [202 kB]
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]
Fetched 15.1 MB in 2s (6260 kB/s)
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
Fetched 2411 kB in 0s (31.6 MB/s)
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Preparing to unpack .../base-files_13.6_arm64.deb ...
Unpacking base-files (13.6) over (13.5) ...
Setting up base-files (13.6) ...
Updating /root/.profile to current default.
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Preparing to unpack .../libapt-pkg6.0t64_2.9.14_arm64.deb ...
Unpacking libapt-pkg6.0t64:arm64 (2.9.14) over (2.9.12) ...
Setting up libapt-pkg6.0t64:arm64 (2.9.14) ...
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Preparing to unpack .../archives/apt_2.9.14_arm64.deb ...
Unpacking apt (2.9.14) over (2.9.12) ...
Setting up apt (2.9.14) ...
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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) ...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/tmp/debusine-fetch-exec-upload-cja7d46h/hilive_2.0a-4.dsc exists in /tmp/debusine-fetch-exec-upload-cja7d46h; copying to chroot
I: NOTICE: Log filtering will replace 'build/hilive-CGer8W/hilive-2.0a' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hilive-CGer8W' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, discount, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, discount, 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
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [794 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [826 B]
Fetched 2229 B in 0s (174 kB/s)
Reading package lists...
Ign:1 file:/<<BUILDDIR>>/resolver-T6e2uA/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-T6e2uA/apt_archive ./ Release [606 B]
Get:2 file:/<<BUILDDIR>>/resolver-T6e2uA/apt_archive ./ Release [606 B]
Ign:3 file:/<<BUILDDIR>>/resolver-T6e2uA/apt_archive ./ Release.gpg
Reading package lists...
Reading package lists...
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 chrpath cmake
cmake-data comerr-dev cpp cpp-14 cpp-14-aarch64-linux-gnu
cpp-aarch64-linux-gnu debhelper dh-autoreconf dh-strip-nondeterminism
discount 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 icu-devtools krb5-multidev libarchive13t64 libasan8
libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-filesystem-dev
libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-iostreams-dev
libboost-iostreams1.83-dev libboost-iostreams1.83.0
libboost-program-options-dev libboost-program-options1.83-dev
libboost-program-options1.83.0 libboost-regex1.83-dev libboost-regex1.83.0
libboost-system-dev libboost-system1.83-dev libboost-system1.83.0
libboost1.83-dev libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0
libcrypt-dev libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl
libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libexpat1
libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev
libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev
libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libicu-dev
libidn2-dev libisl23 libitm1 libjsoncpp26 libkadm5clnt-mit12
libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev libldap-dev liblsan0 liblz4-dev
liblzma-dev libmpc3 libmpfr6 libncursesw6 libnghttp2-dev libnghttp3-dev
libngtcp2-crypto-gnutls-dev libngtcp2-dev libp11-kit-dev libpkgconf3
libproc2-0 libpsl-dev librhash1 librtmp-dev libseqan2-dev libssh2-1-dev
libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1
libunbound8 libuv1t64 libzstd-dev linux-libc-dev m4 nettle-dev pkgconf
pkgconf-bin po-debconf procps rpcsvc-proto zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build doc-base 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 krb5-doc lrzip libboost1.83-doc
libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev
libboost-contract1.83-dev libboost-coroutine1.83-dev
libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev
libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-json1.83-dev
libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
libboost-numpy1.83-dev libboost-python1.83-dev libboost-random1.83-dev
libboost-serialization1.83-dev libboost-stacktrace1.83-dev
libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev
libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev
libboost1.83-tools-dev libmpfrc++-dev libntl-dev libc-devtools glibc-doc
libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data
gnutls-bin gnutls-doc krb5-user icu-doc liblzma-doc libnghttp2-doc
p11-kit-doc libssl-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 libtasn1-doc
libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential chrpath cmake
cmake-data comerr-dev cpp cpp-14 cpp-14-aarch64-linux-gnu
cpp-aarch64-linux-gnu debhelper dh-autoreconf dh-strip-nondeterminism
discount 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 icu-devtools krb5-multidev libarchive13t64 libasan8
libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-filesystem-dev
libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-iostreams-dev
libboost-iostreams1.83-dev libboost-iostreams1.83.0
libboost-program-options-dev libboost-program-options1.83-dev
libboost-program-options1.83.0 libboost-regex1.83-dev libboost-regex1.83.0
libboost-system-dev libboost-system1.83-dev libboost-system1.83.0
libboost1.83-dev libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0
libcrypt-dev libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl
libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libexpat1
libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev
libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev
libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libicu-dev
libidn2-dev libisl23 libitm1 libjsoncpp26 libkadm5clnt-mit12
libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev libldap-dev liblsan0 liblz4-dev
liblzma-dev libmpc3 libmpfr6 libncursesw6 libnghttp2-dev libnghttp3-dev
libngtcp2-crypto-gnutls-dev libngtcp2-dev libp11-kit-dev libpkgconf3
libproc2-0 libpsl-dev librhash1 librtmp-dev libseqan2-dev libssh2-1-dev
libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1
libunbound8 libuv1t64 libzstd-dev linux-libc-dev m4 nettle-dev pkgconf
pkgconf-bin po-debconf procps rpcsvc-proto sbuild-build-depends-main-dummy
zlib1g-dev
0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded.
Need to get 115 MB/116 MB of archives.
After this operation, 603 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B]
Get:2 file:/<<BUILDDIR>>/resolver-T6e2uA/apt_archive ./ libseqan2-dev 2.5.0~rc3+dfsg-1 [1222 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2+b1 [125 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.9-1 [2459 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b2 [680 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b3 [50.5 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8 [9166 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-8 [1284 B]
Get:21 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
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Get:24 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:32 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:34 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:35 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB]
Get:37 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:39 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:40 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:41 http://deb.debian.org/debian sid/main arm64 chrpath arm64 0.18-1 [13.2 kB]
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]
Get:44 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB]
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 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:56 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 discount arm64 2.2.7-2.1 [24.5 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 icu-devtools arm64 72.1-5+b1 [195 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB]
Get:70 http://deb.debian.org/debian sid/main arm64 libboost-atomic1.83.0 arm64 1.83.0-3.2+b1 [234 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libboost-atomic1.83-dev arm64 1.83.0-3.2+b1 [234 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-3.2+b1 [273 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 libboost-system1.83.0 arm64 1.83.0-3.2+b1 [231 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 libboost-system1.83-dev arm64 1.83.0-3.2+b1 [232 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-3.2+b1 [293 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B]
Get:77 http://deb.debian.org/debian sid/main arm64 libboost-regex1.83.0 arm64 1.83.0-3.2+b1 [314 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 libicu-dev arm64 72.1-5+b1 [10.3 MB]
Get:79 http://deb.debian.org/debian sid/main arm64 libboost-regex1.83-dev arm64 1.83.0-3.2+b1 [335 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-3.2+b1 [251 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-3.2+b1 [261 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B]
Get:83 http://deb.debian.org/debian sid/main arm64 libboost-program-options1.83.0 arm64 1.83.0-3.2+b1 [331 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 libboost-program-options1.83-dev arm64 1.83.0-3.2+b1 [369 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B]
Get:86 http://deb.debian.org/debian sid/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B]
Get:87 http://deb.debian.org/debian sid/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 libunbound8 arm64 1.22.0-1 [553 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 liblz4-dev arm64 1.9.4-3+b1 [79.1 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 chrpath_0.18-1 cmake_3.31.1-1 cmake-data_3.31.1-1 comerr-dev_2.1-1.47.1-1+b1 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 discount_2.2.7-2.1 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 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libparams-util-perl_1.102-3+b1 libpath-tiny-perl_0.146-1 libpcre2-8-0_10.44-4 libperl5.40_5.40.0-7 libperlio-gzip-perl_0.20-1+b4 libperlio-utf8-strict-perl_0.010-1+b3 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libproc-processtable-perl_0.636-1+b3 libproc2-0_2:4.0.4-6 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libreadline8t64_8.2-5 libregexp-wildcards-perl_1.05-3 librhash1_1.4.5-1 librole-tiny-perl_2.002004-1 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b3 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libseqan2-dev_2.5.0~rc3+dfsg-1 libsereal-decoder-perl_5.004+ds-1+b3 libsereal-encoder-perl_5.004+ds-1+b3 libsframe1_2.43.1-5 libsmartcols1_2.40.2-11 libsort-versions-perl_1.62-3 libsqlite3-0_3.46.1-1 libss2_1.47.1-1+b1 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.3.2-2 libssl3t64_3.3.2-2 libstdc++-14-dev_14.2.0-8 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libwww-robotrules-perl_6.02-1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-5+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-4 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxmlb2_0.3.21-1 libxs-parse-keyword-perl_0.46-1+b1 libxxhash0_0.8.2-2+b2 libyaml-0-2_0.2.5-1+b2 libyaml-libyaml-perl_0.902.0+ds-2+b1 libzstd-dev_1.5.6+dfsg-1+b1 libzstd1_1.5.6+dfsg-1+b1 lintian_2.120.0 linux-libc-dev_6.11.9-1 login_1:4.16.0-2+really2.40.2-11 login.defs_1:4.16.0-5 logsave_1.47.1-1+b1 lzop_1.04-2+b1 m4_1.4.19-4 make_4.3-4.1+b1 man-db_2.13.0-1 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 nettle-dev_3.10-1+b1 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 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 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
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: hilive
Binary: hilive
Architecture: any
Version: 2.0a-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://gitlab.com/rki_bioinformatics/HiLive2
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/hilive
Vcs-Git: https://salsa.debian.org/med-team/hilive.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, discount
Package-List:
hilive deb science optional arch=any
Checksums-Sha1:
5705773f60eef87916fe3612b26df04ae3959d32 161788 hilive_2.0a.orig.tar.gz
ed28dc5d15857303f512465c47adc3a9aa32ef3d 9160 hilive_2.0a-4.debian.tar.xz
Checksums-Sha256:
a60e7675988b35d9ebf9472ca7515b40f790654c04e67d35fabf069d91d73bf6 161788 hilive_2.0a.orig.tar.gz
04497470e67f179dad42efb1d3773e9f84904c13b79fbfc8600508f084fbb3c6 9160 hilive_2.0a-4.debian.tar.xz
Files:
8d393041a814071b4ac6a3db1f1f10e6 161788 hilive_2.0a.orig.tar.gz
93489243120b9716f0e6696b85e2b2bd 9160 hilive_2.0a-4.debian.tar.xz
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gpgv: Signature made Thu Jun 13 23:47:02 2024 UTC
gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
gpgv: issuer "plessy@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./hilive_2.0a-4.dsc: no acceptable signature found
dpkg-source: info: extracting hilive in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hilive_2.0a.orig.tar.gz
dpkg-source: info: unpacking hilive_2.0a-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying do_not_set_rpath.patch
dpkg-source: info: applying use_FindSeQan.patch
dpkg-source: info: applying use_dynamic_linking.patch
dpkg-source: info: applying remove_march_native.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 hilive
dpkg-buildpackage: info: source version 2.0a-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Charles Plessy <plessy@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DSEQAN_PATH=/usr/lib/seqan/
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 -DSEQAN_PATH=/usr/lib/seqan/ ..
-- 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
CMake Warning (dev) at CMakeLists.txt:81 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: system filesystem program_options iostreams
-- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1")
-- Performing Test CXX14_BUILTIN
-- Performing Test CXX14_BUILTIN - Success
-- Looking for C++ include execinfo.h
-- Looking for C++ include execinfo.h - found
-- Found SeqAn: /usr/include (found version "2.5.0")
-- Configuring done (1.9s)
-- 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
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build
cd obj-aarch64-linux-gnu && make -j8 "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/HiLiveLibs.dir/build.make CMakeFiles/HiLiveLibs.dir/depend
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[ 18%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o
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[ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o
[ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o
[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o
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/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu -I/<<PKGBUILDDIR>>/lib -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 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -c /<<PKGBUILDDIR>>/lib/parallel.cpp
In file included from /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/tools_static.h:10,
from /<<PKGBUILDDIR>>/lib/tools_static.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/tools_static.h:10,
from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/tools.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/kindex.h:4,
from /<<PKGBUILDDIR>>/lib/kindex.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/alnstream.h:4,
from /<<PKGBUILDDIR>>/lib/alnstream.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/alnread.h:4,
from /<<PKGBUILDDIR>>/lib/alnread.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/parallel.h:4,
from /<<PKGBUILDDIR>>/lib/parallel.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/illumina_parsers.h:4,
from /<<PKGBUILDDIR>>/lib/illumina_parsers.cpp:1:
/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 /usr/include/seqan/align.h:151,
from /usr/include/seqan/bam_io.h:50,
from /<<PKGBUILDDIR>>/lib/headers.h:39,
from /<<PKGBUILDDIR>>/lib/alnout.h:4,
from /<<PKGBUILDDIR>>/lib/alnout.cpp:1:
/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>>
| ^~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/kindex.h:7:
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/kindex.h:7,
from /<<PKGBUILDDIR>>/lib/alnstream.h:7:
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
In file included from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/kindex.h:7,
from /<<PKGBUILDDIR>>/lib/alnread.h:6:
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools.cpp:7:1: error: ‘seqan’ does not name a type
7 | seqan::BamHeader getBamHeader() {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
In file included from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/parallel.h:6:
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/kindex.h:7,
from /<<PKGBUILDDIR>>/lib/alnout.h:7:
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /<<PKGBUILDDIR>>/lib/tools.h:11,
from /<<PKGBUILDDIR>>/lib/illumina_parsers.h:6:
/<<PKGBUILDDIR>>/lib/tools_static.h:39:42: error: ‘seqan’ does not name a type
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h:39:68: error: expected unqualified-id before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h:39:67: error: expected ‘)’ before ‘&’ token
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ~ ^~
| )
/<<PKGBUILDDIR>>/lib/tools_static.h:39:70: error: expected initializer before ‘l’
39 | inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
| ^
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void ltrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:304:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/lib/headers.h:1:
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools_static.h: In function ‘void rtrim(std::string&)’:
/<<PKGBUILDDIR>>/lib/tools_static.h:314:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here
1123 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/tools.h: At global scope:
/<<PKGBUILDDIR>>/lib/tools.h:137:1: error: ‘seqan’ does not name a type
137 | seqan::BamHeader getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:15:9: error: ‘seqan’ does not name a type
15 | typedef seqan::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:20:9: error: ‘seqan’ does not name a type
20 | typedef seqan::Index<seqan::StringSet<seqan::DnaString>, seqan::FMIndex<void, FMIConfig> > FMIndex;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:25:9: error: ‘seqan’ does not name a type
25 | typedef seqan::Iterator<FMIndex, seqan::TopDown<> >::Type FMTopDownIterator;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:30:9: error: ‘seqan’ does not name a type
30 | typedef seqan::Iter<FMIndex,seqan::VSTree<seqan::TopDown<seqan::Preorder>>>::TVertexDesc FMVertexDescriptor;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:15:9: error: ‘seqan’ does not name a type
15 | typedef seqan::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:20:9: error: ‘seqan’ does not name a type
20 | typedef seqan::Index<seqan::StringSet<seqan::DnaString>, seqan::FMIndex<void, FMIConfig> > FMIndex;
| ^~~~~
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:82: CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
/<<PKGBUILDDIR>>/lib/kindex.h:25:9: error: ‘seqan’ does not name a type
25 | typedef seqan::Iterator<FMIndex, seqan::TopDown<> >::Type FMTopDownIterator;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:30: error: ‘FMVertexDescriptor’ does not name a type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:52: error: ‘FMVertexDescriptor’ has not been declared
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:13: error: ‘bool operator==(int, int)’ must have an argument of class or enumerated type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:30:9: error: ‘seqan’ does not name a type
30 | typedef seqan::Iter<FMIndex,seqan::VSTree<seqan::TopDown<seqan::Preorder>>>::TVertexDesc FMVertexDescriptor;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:15:9: error: ‘seqan’ does not name a type
15 | typedef seqan::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:20:9: error: ‘seqan’ does not name a type
20 | typedef seqan::Index<seqan::StringSet<seqan::DnaString>, seqan::FMIndex<void, FMIConfig> > FMIndex;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:25:9: error: ‘seqan’ does not name a type
25 | typedef seqan::Iterator<FMIndex, seqan::TopDown<> >::Type FMTopDownIterator;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:30:9: error: ‘seqan’ does not name a type
30 | typedef seqan::Iter<FMIndex,seqan::VSTree<seqan::TopDown<seqan::Preorder>>>::TVertexDesc FMVertexDescriptor;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:30: error: ‘FMVertexDescriptor’ does not name a type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:52: error: ‘FMVertexDescriptor’ has not been declared
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:13: error: ‘bool operator==(int, int)’ must have an argument of class or enumerated type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:29: error: ‘FMVertexDescriptor’ does not name a type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:51: error: ‘FMVertexDescriptor’ has not been declared
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:13: error: ‘bool operator<(int, int)’ must have an argument of class or enumerated type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:30: error: ‘FMVertexDescriptor’ does not name a type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:52: error: ‘FMVertexDescriptor’ has not been declared
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:13: error: ‘bool operator==(int, int)’ must have an argument of class or enumerated type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:29: error: ‘FMVertexDescriptor’ does not name a type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:51: error: ‘FMVertexDescriptor’ has not been declared
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:13: error: ‘bool operator<(int, int)’ must have an argument of class or enumerated type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:29: error: ‘FMVertexDescriptor’ does not name a type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:51: error: ‘FMVertexDescriptor’ has not been declared
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:13: error: ‘bool operator>(int, int)’ must have an argument of class or enumerated type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:29: error: ‘FMVertexDescriptor’ does not name a type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:51: error: ‘FMVertexDescriptor’ has not been declared
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:13: error: ‘bool operator<(int, int)’ must have an argument of class or enumerated type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:29: error: ‘FMVertexDescriptor’ does not name a type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:51: error: ‘FMVertexDescriptor’ has not been declared
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:13: error: ‘bool operator>(int, int)’ must have an argument of class or enumerated type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:30: error: ‘FMVertexDescriptor’ does not name a type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:52: error: ‘FMVertexDescriptor’ has not been declared
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:13: error: ‘bool operator!=(int, int)’ must have an argument of class or enumerated type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:79:9: error: ‘seqan’ does not name a type
79 | seqan::StringSet<seqan::DnaString> seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:100:26: error: ‘FMIndex’ has not been declared
100 | int save_fmindex(FMIndex & idx, const std::string &iname);
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:207:9: error: ‘FMIndex’ does not name a type
207 | FMIndex idx;
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp: In member function ‘int KixBuild::create_index(const std::string&, const std::string&, bool, bool)’:
/<<PKGBUILDDIR>>/lib/kindex.cpp:26:9: error: ‘seqan’ has not been declared
26 | seqan::StringSet<seqan::DnaString> all_seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:26:26: error: ‘seqan’ has not been declared
26 | seqan::StringSet<seqan::DnaString> all_seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:29: error: ‘FMVertexDescriptor’ does not name a type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:51: error: ‘FMVertexDescriptor’ has not been declared
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:13: error: ‘bool operator>(int, int)’ must have an argument of class or enumerated type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:30: error: ‘FMVertexDescriptor’ does not name a type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:52: error: ‘FMVertexDescriptor’ has not been declared
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:13: error: ‘bool operator!=(int, int)’ must have an argument of class or enumerated type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:26:44: error: ‘all_seqs’ was not declared in this scope
26 | seqan::StringSet<seqan::DnaString> all_seqs;
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:79:9: error: ‘seqan’ does not name a type
79 | seqan::StringSet<seqan::DnaString> seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:100:26: error: ‘FMIndex’ has not been declared
100 | int save_fmindex(FMIndex & idx, const std::string &iname);
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:207:9: error: ‘FMIndex’ does not name a type
207 | FMIndex idx;
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:28:40: error: ‘seqs’ was not declared in this scope
28 | for(uint16_t i = 0; i < length(seqs); i++) {
| ^~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:28:33: error: ‘length’ was not declared in this scope
28 | for(uint16_t i = 0; i < length(seqs); i++) {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:28:33: note: suggested alternatives:
In file included from /usr/include/seqan/index/index_pizzachili.h:39,
from /usr/include/seqan/index.h:194,
from /<<PKGBUILDDIR>>/lib/kindex.h:9:
/usr/include/seqan/index/index_pizzachili_string.h:376:1: note: ‘seqan2::length’
376 | length(String<TValue, PizzaChili<TSpec> > const& me) {
| ^~~~~~
In file included from /usr/include/boost/tuple/tuple.hpp:28,
from /usr/include/boost/multi_index/detail/index_base.hpp:30,
from /usr/include/boost/multi_index/detail/base_type.hpp:21,
from /usr/include/boost/multi_index_container.hpp:36,
from /usr/include/boost/property_tree/ptree.hpp:21,
from /usr/include/boost/property_tree/xml_parser.hpp:14,
from /<<PKGBUILDDIR>>/lib/headers.h:30:
/usr/include/boost/tuple/detail/tuple_basic.hpp:86:26: note: ‘boost::tuples::length’
86 | template<class T> struct length;
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:30: error: ‘FMVertexDescriptor’ does not name a type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/algorithm/string/trim.hpp:19,
from /usr/include/boost/algorithm/string.hpp:19,
from /<<PKGBUILDDIR>>/lib/headers.h:35:
/usr/include/boost/range/as_literal.hpp:57:28: note: ‘boost::range_detail::length’
57 | inline std::size_t length( const wchar_t* s )
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:29:17: error: ‘seqan’ has not been declared
29 | seqan::ModifiedString<seqan::DnaString, seqan::ModReverse> rev(seqs[i]);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:29:39: error: ‘seqan’ has not been declared
29 | seqan::ModifiedString<seqan::DnaString, seqan::ModReverse> rev(seqs[i]);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:29:57: error: ‘seqan’ has not been declared
29 | seqan::ModifiedString<seqan::DnaString, seqan::ModReverse> rev(seqs[i]);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:52: error: ‘FMVertexDescriptor’ has not been declared
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:13: error: ‘bool operator!=(int, int)’ must have an argument of class or enumerated type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:96: CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o] Error 1
In file included from /<<PKGBUILDDIR>>/lib/parallel.h:7:
/<<PKGBUILDDIR>>/lib/kindex.h:15:9: error: ‘seqan’ does not name a type
15 | typedef seqan::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:15:9: error: ‘seqan’ does not name a type
15 | typedef seqan::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:79:9: error: ‘seqan’ does not name a type
79 | seqan::StringSet<seqan::DnaString> seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:100:26: error: ‘FMIndex’ has not been declared
100 | int save_fmindex(FMIndex & idx, const std::string &iname);
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:20:9: error: ‘seqan’ does not name a type
20 | typedef seqan::Index<seqan::StringSet<seqan::DnaString>, seqan::FMIndex<void, FMIConfig> > FMIndex;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:20:9: error: ‘seqan’ does not name a type
20 | typedef seqan::Index<seqan::StringSet<seqan::DnaString>, seqan::FMIndex<void, FMIConfig> > FMIndex;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:25:9: error: ‘seqan’ does not name a type
25 | typedef seqan::Iterator<FMIndex, seqan::TopDown<> >::Type FMTopDownIterator;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:25:9: error: ‘seqan’ does not name a type
25 | typedef seqan::Iterator<FMIndex, seqan::TopDown<> >::Type FMTopDownIterator;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:207:9: error: ‘FMIndex’ does not name a type
207 | FMIndex idx;
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:29:76: error: ‘rev’ was not declared in this scope
29 | seqan::ModifiedString<seqan::DnaString, seqan::ModReverse> rev(seqs[i]);
| ^~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:30:17: error: ‘seqan’ has not been declared
30 | seqan::appendValue(all_seqs, rev);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:31:17: error: ‘seqan’ has not been declared
31 | seqan::complement(seqs[i]);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:32:17: error: ‘seqan’ has not been declared
32 | seqan::appendValue(all_seqs, seqs[i]);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:30:9: error: ‘seqan’ does not name a type
30 | typedef seqan::Iter<FMIndex,seqan::VSTree<seqan::TopDown<seqan::Preorder>>>::TVertexDesc FMVertexDescriptor;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:30:9: error: ‘seqan’ does not name a type
30 | typedef seqan::Iter<FMIndex,seqan::VSTree<seqan::TopDown<seqan::Preorder>>>::TVertexDesc FMVertexDescriptor;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:36:9: error: ‘FMIndex’ was not declared in this scope; did you mean ‘seqan2::FMIndex’?
36 | FMIndex idx(all_seqs);
| ^~~~~~~
| 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>>/lib/kindex.cpp:39:15: error: ‘seqan’ has not been declared
39 | if( ! seqan::indexCreate(idx) )
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:43:27: error: invalid conversion from ‘KixRun*’ to ‘int’ [-fpermissive]
43 | if ( save_fmindex(idx, iname) != 1 )
| ^~~
| |
| KixRun*
/<<PKGBUILDDIR>>/lib/kindex.h:100:36: note: initializing argument 1 of ‘int KixBuild::save_fmindex(int&, const std::string&)’
100 | int save_fmindex(FMIndex & idx, const std::string &iname);
| ~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:43:27: error: cannot bind rvalue ‘(int)idx’ to ‘int&’
43 | if ( save_fmindex(idx, iname) != 1 )
| ^~~
/<<PKGBUILDDIR>>/lib/kindex.cpp: In member function ‘int KixBuild::add_fasta(const std::string&, bool, bool)’:
/<<PKGBUILDDIR>>/lib/kindex.cpp:64:3: error: ‘seqan’ has not been declared
64 | seqan::DnaString newSeq = ""; // current DNA sequence
| ^~~~~
In file included from /<<PKGBUILDDIR>>/lib/alnstream.h:9:
/<<PKGBUILDDIR>>/lib/alnread.h:23:9: error: ‘FMVertexDescriptor’ does not name a type
23 | FMVertexDescriptor vDesc;
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:42:9: error: ‘seqan’ does not name a type
42 | seqan::String<seqan::CigarElement<> > returnSeqanCigarString() const;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:81:24: error: ‘newSeq’ was not declared in this scope
81 | if ( newSeq != "" ) {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:82:27: error: ‘seqan’ has not been declared
82 | seqan::appendValue(seqs, newSeq);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:23:9: error: ‘FMVertexDescriptor’ does not name a type
23 | FMVertexDescriptor vDesc;
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:30: error: ‘FMVertexDescriptor’ does not name a type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:52: error: ‘FMVertexDescriptor’ has not been declared
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:13: error: ‘bool operator==(int, int)’ must have an argument of class or enumerated type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:30: error: ‘FMVertexDescriptor’ does not name a type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:52: error: ‘FMVertexDescriptor’ has not been declared
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:32:13: error: ‘bool operator==(int, int)’ must have an argument of class or enumerated type
32 | inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:82:46: error: ‘seqs’ was not declared in this scope
82 | seqan::appendValue(seqs, newSeq);
| ^~~~
/<<PKGBUILDDIR>>/lib/alnread.h: In member function ‘CountType Seed::getNumPositions() const’:
/<<PKGBUILDDIR>>/lib/alnread.h:105:24: error: ‘vDesc’ was not declared in this scope
105 | return vDesc.range.i2 - vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:42:9: error: ‘seqan’ does not name a type
42 | seqan::String<seqan::CigarElement<> > returnSeqanCigarString() const;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: In function ‘bool operator<(Seed, Seed)’:
/<<PKGBUILDDIR>>/lib/alnread.h:196:16: error: ‘const struct Seed’ has no member named ‘vDesc’
196 | if ( l.vDesc != r.vDesc ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:196:27: error: ‘const struct Seed’ has no member named ‘vDesc’
196 | if ( l.vDesc != r.vDesc ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:197:26: error: ‘const struct Seed’ has no member named ‘vDesc’
197 | return l.vDesc < r.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:197:36: error: ‘const struct Seed’ has no member named ‘vDesc’
197 | return l.vDesc < r.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: At global scope:
/<<PKGBUILDDIR>>/lib/alnread.h:255:71: error: ‘FMTopDownIterator’ has not been declared
255 | void getMatchSeeds(CountType read_base, CountType index_base, FMTopDownIterator & it, USeed origin, SeedVec & newSeeds);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:274:74: error: ‘FMTopDownIterator’ has not been declared
274 | void getDeletionSeeds(CountType read_base, CountType index_base, FMTopDownIterator & it, USeed origin, SeedVec & newSeeds);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:410:34: error: ‘seqan’ has not been declared
410 | void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:410:60: error: expected ‘,’ or ‘...’ before ‘&’ token
410 | void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
| ^
/<<PKGBUILDDIR>>/lib/kindex.cpp:103:19: error: ‘newSeq’ was not declared in this scope
103 | newSeq = "";
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:29: error: ‘FMVertexDescriptor’ does not name a type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:51: error: ‘FMVertexDescriptor’ has not been declared
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:13: error: ‘bool operator<(int, int)’ must have an argument of class or enumerated type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:29: error: ‘FMVertexDescriptor’ does not name a type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:51: error: ‘FMVertexDescriptor’ has not been declared
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:36:13: error: ‘bool operator<(int, int)’ must have an argument of class or enumerated type
36 | inline bool operator<(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: In member function ‘CountType Seed::getNumPositions() const’:
/<<PKGBUILDDIR>>/lib/alnread.h:105:24: error: ‘vDesc’ was not declared in this scope
105 | return vDesc.range.i2 - vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:112:27: error: ‘newSeq’ was not declared in this scope
112 | newSeq = line;
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnstream.cpp: In member function ‘uint64_t oAlnStream::lz4write(const char*, uint64_t)’:
/<<PKGBUILDDIR>>/lib/alnstream.cpp:23:43: warning: ‘int LZ4_compress(const char*, char*, int)’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations]
23 | uint32_t compressed_size = LZ4_compress (source, buf.data(), size);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/lib/headers.h:5:
/usr/include/lz4.h:765:75: note: declared here
765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize);
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: In function ‘bool operator<(Seed, Seed)’:
/<<PKGBUILDDIR>>/lib/alnread.h:196:16: error: ‘const struct Seed’ has no member named ‘vDesc’
196 | if ( l.vDesc != r.vDesc ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:196:27: error: ‘const struct Seed’ has no member named ‘vDesc’
196 | if ( l.vDesc != r.vDesc ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:197:26: error: ‘const struct Seed’ has no member named ‘vDesc’
197 | return l.vDesc < r.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:197:36: error: ‘const struct Seed’ has no member named ‘vDesc’
197 | return l.vDesc < r.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: At global scope:
/<<PKGBUILDDIR>>/lib/alnread.h:255:71: error: ‘FMTopDownIterator’ has not been declared
255 | void getMatchSeeds(CountType read_base, CountType index_base, FMTopDownIterator & it, USeed origin, SeedVec & newSeeds);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:274:74: error: ‘FMTopDownIterator’ has not been declared
274 | void getDeletionSeeds(CountType read_base, CountType index_base, FMTopDownIterator & it, USeed origin, SeedVec & newSeeds);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:410:34: error: ‘seqan’ has not been declared
410 | void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:410:60: error: expected ‘,’ or ‘...’ before ‘&’ token
410 | void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
| ^
/<<PKGBUILDDIR>>/lib/alnread.cpp:4:1: error: ‘seqan’ does not name a type
4 | seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:118:27: error: ‘newSeq’ was not declared in this scope
118 | newSeq += line;
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:29: error: ‘FMVertexDescriptor’ does not name a type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:51: error: ‘FMVertexDescriptor’ has not been declared
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:13: error: ‘bool operator>(int, int)’ must have an argument of class or enumerated type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:29: error: ‘FMVertexDescriptor’ does not name a type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:51: error: ‘FMVertexDescriptor’ has not been declared
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:42:13: error: ‘bool operator>(int, int)’ must have an argument of class or enumerated type
42 | inline bool operator>(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:152: CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o] Error 1
/<<PKGBUILDDIR>>/lib/kindex.cpp:127:8: error: ‘newSeq’ was not declared in this scope
127 | if ( newSeq != "" ) {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:128:11: error: ‘seqan’ has not been declared
128 | seqan::appendValue(seqs, newSeq);
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:128:30: error: ‘seqs’ was not declared in this scope
128 | seqan::appendValue(seqs, newSeq);
| ^~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp: At global scope:
/<<PKGBUILDDIR>>/lib/kindex.cpp:135:5: error: ‘int KixBuild::save_fmindex’ is not a static data member of ‘class KixBuild’
135 | int KixBuild::save_fmindex( FMIndex & idx, const std::string &iname ) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:135:29: error: ‘FMIndex’ was not declared in this scope; did you mean ‘seqan2::FMIndex’?
135 | int KixBuild::save_fmindex( FMIndex & idx, const std::string &iname ) {
| ^~~~~~~
| seqan2::FMIndex
/usr/include/seqan/index/index_fm.h:143:7: note: ‘seqan2::FMIndex’ declared here
143 | class FMIndex;
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:135:44: error: expected primary-expression before ‘const’
135 | int KixBuild::save_fmindex( FMIndex & idx, const std::string &iname ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.cpp:135:69: error: expression list treated as compound expression in initializer [-fpermissive]
135 | int KixBuild::save_fmindex( FMIndex & idx, const std::string &iname ) {
| ^
/<<PKGBUILDDIR>>/lib/kindex.cpp: In member function ‘int KixRun::load_fmindex(std::string)’:
/<<PKGBUILDDIR>>/lib/kindex.cpp:230:14: error: ‘seqan’ has not been declared
230 | if ( seqan::open(idx, filename) != 1 ) // function returns 1 on success
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:30: error: ‘FMVertexDescriptor’ does not name a type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:52: error: ‘FMVertexDescriptor’ has not been declared
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:13: error: ‘bool operator!=(int, int)’ must have an argument of class or enumerated type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:30: error: ‘FMVertexDescriptor’ does not name a type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:52: error: ‘FMVertexDescriptor’ has not been declared
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:48:13: error: ‘bool operator!=(int, int)’ must have an argument of class or enumerated type
48 | inline bool operator!=(const FMVertexDescriptor l, FMVertexDescriptor r) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘uint16_t Seed::serialize_size() const’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:97:24: error: ‘FMVertexDescriptor’ was not declared in this scope
97 | total_size += sizeof(FMVertexDescriptor);
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:79:9: error: ‘seqan’ does not name a type
79 | seqan::StringSet<seqan::DnaString> seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:100:26: error: ‘FMIndex’ has not been declared
100 | int save_fmindex(FMIndex & idx, const std::string &iname);
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:79:9: error: ‘seqan’ does not name a type
79 | seqan::StringSet<seqan::DnaString> seqs;
| ^~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:100:26: error: ‘FMIndex’ has not been declared
100 | int save_fmindex(FMIndex & idx, const std::string &iname);
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:207:9: error: ‘FMIndex’ does not name a type
207 | FMIndex idx;
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/kindex.h:207:9: error: ‘FMIndex’ does not name a type
207 | FMIndex idx;
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘std::vector<char> Seed::serialize()’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:135:13: error: ‘vDesc’ was not declared in this scope
135 | memcpy(d,&vDesc,sizeof(FMVertexDescriptor));
| ^~~~~
In file included from /<<PKGBUILDDIR>>/lib/alnstream.h:9,
from /<<PKGBUILDDIR>>/lib/alnout.h:9:
/<<PKGBUILDDIR>>/lib/alnread.h:23:9: error: ‘FMVertexDescriptor’ does not name a type
23 | FMVertexDescriptor vDesc;
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:42:9: error: ‘seqan’ does not name a type
42 | seqan::String<seqan::CigarElement<> > returnSeqanCigarString() const;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:135:26: error: ‘FMVertexDescriptor’ was not declared in this scope
135 | memcpy(d,&vDesc,sizeof(FMVertexDescriptor));
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: In member function ‘CountType Seed::getNumPositions() const’:
/<<PKGBUILDDIR>>/lib/alnread.h:105:24: error: ‘vDesc’ was not declared in this scope
105 | return vDesc.range.i2 - vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: In function ‘bool operator<(Seed, Seed)’:
/<<PKGBUILDDIR>>/lib/alnread.h:196:16: error: ‘const struct Seed’ has no member named ‘vDesc’
196 | if ( l.vDesc != r.vDesc ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:196:27: error: ‘const struct Seed’ has no member named ‘vDesc’
196 | if ( l.vDesc != r.vDesc ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:197:26: error: ‘const struct Seed’ has no member named ‘vDesc’
197 | return l.vDesc < r.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:197:36: error: ‘const struct Seed’ has no member named ‘vDesc’
197 | return l.vDesc < r.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘uint16_t Seed::deserialize(char*)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:180:11: error: ‘vDesc’ was not declared in this scope
180 | memcpy(&vDesc,d+bytes,sizeof(FMVertexDescriptor));
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h: At global scope:
/<<PKGBUILDDIR>>/lib/alnread.h:255:71: error: ‘FMTopDownIterator’ has not been declared
255 | void getMatchSeeds(CountType read_base, CountType index_base, FMTopDownIterator & it, USeed origin, SeedVec & newSeeds);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:274:74: error: ‘FMTopDownIterator’ has not been declared
274 | void getDeletionSeeds(CountType read_base, CountType index_base, FMTopDownIterator & it, USeed origin, SeedVec & newSeeds);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:410:34: error: ‘seqan’ has not been declared
410 | void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.h:410:60: error: expected ‘,’ or ‘...’ before ‘&’ token
410 | void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:23:9: error: ‘seqan’ does not name a type
23 | seqan::BamFileOut bfo;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:58:27: error: ‘seqan’ has not been declared
58 | void setContext ( seqan::BamIOContext<seqan::StringSet<seqan::CharString> > & context ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:58:46: error: expected ‘,’ or ‘...’ before ‘<’ token
58 | void setContext ( seqan::BamIOContext<seqan::StringSet<seqan::CharString> > & context ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:66:28: error: ‘seqan’ has not been declared
66 | void writeHeader ( seqan::BamHeader & header ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:66:45: error: expected ‘,’ or ‘...’ before ‘&’ token
66 | void writeHeader ( seqan::BamHeader & header ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:74:41: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:74:66: error: template argument 1 is invalid
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:74:66: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:180:32: error: ‘FMVertexDescriptor’ was not declared in this scope
180 | memcpy(&vDesc,d+bytes,sizeof(FMVertexDescriptor));
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:74:41: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:74:66: error: template argument 1 is invalid
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:74:66: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘std::vector<GenomePosType> Seed::getPositions(CountType, CountType) const’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:376:36: error: ‘vDesc’ was not declared in this scope
376 | CountType seed_positions = vDesc.range.i2 - vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:74:41: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:74:66: error: template argument 1 is invalid
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:74:66: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:74:34: error: ‘std::vector’ is not a type
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:74:40: error: expected ‘,’ or ‘...’ before ‘<’ token
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:383:9: error: ‘FMVertexDescriptor’ was not declared in this scope
383 | FMVertexDescriptor sub_vDesc = vDesc;
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:386:17: error: ‘sub_vDesc’ was not declared in this scope
386 | sub_vDesc.range.i1 += firstPosition;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:389:17: error: ‘sub_vDesc’ was not declared in this scope
389 | sub_vDesc.range.i2 = vDesc.range.i1 + lastPosition;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:392:9: error: ‘FMTopDownIterator’ was not declared in this scope
392 | FMTopDownIterator it(idx->idx, sub_vDesc);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:398:26: error: ‘seqan’ has not been declared
398 | auto positions = seqan::getOccurrences(it);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:398:48: error: ‘it’ was not declared in this scope; did you mean ‘int’?
398 | auto positions = seqan::getOccurrences(it);
| ^~
| int
/<<PKGBUILDDIR>>/lib/alnread.cpp:399:35: error: ‘seqan’ has not been declared
399 | CountType sub_positions = seqan::length(positions);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::extendSeed(char, USeed, SeedVec&)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:649:41: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
649 | uint64_t origin_range = origin->vDesc.range.i2 - origin->vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:649:66: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
649 | uint64_t origin_range = origin->vDesc.range.i2 - origin->vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:658:17: error: ‘FMTopDownIterator’ was not declared in this scope
658 | FMTopDownIterator it(idx->idx, origin->vDesc);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:659:22: error: ‘seqan’ has not been declared
659 | if ( seqan::goDown(it, seqan::DnaString(base)) ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:659:36: error: ‘it’ was not declared in this scope; did you mean ‘int’?
659 | if ( seqan::goDown(it, seqan::DnaString(base)) ) {
| ^~
| int
/<<PKGBUILDDIR>>/lib/alnread.cpp:659:40: error: ‘seqan’ has not been declared
659 | if ( seqan::goDown(it, seqan::DnaString(base)) ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:684:17: error: ‘FMTopDownIterator’ was not declared in this scope
684 | FMTopDownIterator it(idx->idx, origin->vDesc);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:686:22: error: ‘seqan’ has not been declared
686 | if ( seqan::goDown(it, seqan::DnaString(index_base)) ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:686:36: error: ‘it’ was not declared in this scope; did you mean ‘int’?
686 | if ( seqan::goDown(it, seqan::DnaString(index_base)) ) {
| ^~
| int
/<<PKGBUILDDIR>>/lib/alnread.cpp:686:40: error: ‘seqan’ has not been declared
686 | if ( seqan::goDown(it, seqan::DnaString(index_base)) ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: At global scope:
/<<PKGBUILDDIR>>/lib/alnread.cpp:702:78: error: ‘FMTopDownIterator’ has not been declared
702 | void ReadAlignment::getMatchSeeds(CountType read_base, CountType index_base, FMTopDownIterator& it, USeed origin, SeedVec & newSeeds) {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::getMatchSeeds(CountType, CountType, int&, USeed, SeedVec&)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:723:12: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
723 | s->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:723:23: error: request for member ‘vDesc’ in ‘it’, which is of non-class type ‘int’
723 | s->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::getInsertionSeeds(USeed, SeedVec&)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:776:20: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
776 | s->vDesc = origin->vDesc; // Use origin since an insertion means to stay at the same index position
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:776:36: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
776 | s->vDesc = origin->vDesc; // Use origin since an insertion means to stay at the same index position
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: At global scope:
/<<PKGBUILDDIR>>/lib/alnread.cpp:793:81: error: ‘FMTopDownIterator’ has not been declared
793 | void ReadAlignment::getDeletionSeeds(CountType read_base, CountType index_base, FMTopDownIterator& it, USeed origin, SeedVec & newSeeds) {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::getDeletionSeeds(CountType, CountType, int&, USeed, SeedVec&)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:820:12: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
820 | s->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:820:23: error: request for member ‘vDesc’ in ‘it’, which is of non-class type ‘int’
820 | s->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::recursive_goDown(CountType, USeed, SeedVec&)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:838:41: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
838 | uint64_t origin_range = origin->vDesc.range.i2 - origin->vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:838:66: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
838 | uint64_t origin_range = origin->vDesc.range.i2 - origin->vDesc.range.i1;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:851:17: error: ‘FMTopDownIterator’ was not declared in this scope
851 | FMTopDownIterator it(idx->idx, origin->vDesc);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:854:29: error: ‘it’ was not declared in this scope; did you mean ‘int’?
854 | if ( goDown(it, seqan::DnaString(revtwobit_repr( base_repr )))) {
| ^~
| int
/<<PKGBUILDDIR>>/lib/alnread.cpp:854:33: error: ‘seqan’ has not been declared
854 | if ( goDown(it, seqan::DnaString(revtwobit_repr( base_repr )))) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:854:22: error: ‘goDown’ was not declared in this scope; did you mean ‘seqan2::goDown’?
854 | if ( goDown(it, seqan::DnaString(revtwobit_repr( base_repr )))) {
| ^~~~~~
| seqan2::goDown
In file included from /usr/include/seqan/index.h:155,
from /<<PKGBUILDDIR>>/lib/kindex.h:9:
/usr/include/seqan/index/index_fm_right_array_binary_tree_iterator.h:393:13: note: ‘seqan2::goDown’ declared here
393 | inline bool goDown(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter)
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:858:28: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
858 | s->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:894:17: error: ‘FMTopDownIterator’ was not declared in this scope
894 | FMTopDownIterator it(idx->idx, origin->vDesc);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:897:29: error: ‘it’ was not declared in this scope; did you mean ‘int’?
897 | if ( goDown(it, seqan::DnaString(revtwobit_repr(b)))) {
| ^~
| int
/<<PKGBUILDDIR>>/lib/alnread.cpp:897:33: error: ‘seqan’ has not been declared
897 | if ( goDown(it, seqan::DnaString(revtwobit_repr(b)))) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:897:22: error: ‘goDown’ was not declared in this scope; did you mean ‘seqan2::goDown’?
897 | if ( goDown(it, seqan::DnaString(revtwobit_repr(b)))) {
| ^~~~~~
| seqan2::goDown
/usr/include/seqan/index/index_fm_right_array_binary_tree_iterator.h:393:13: note: ‘seqan2::goDown’ declared here
393 | inline bool goDown(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter)
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:901:28: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
901 | s->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::createSeeds(SeedVec&)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:928:9: error: ‘FMTopDownIterator’ was not declared in this scope
928 | FMTopDownIterator it(idx->idx);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:929:14: error: ‘seqan’ has not been declared
929 | if ( seqan::goDown(it, seqan::Dna5String(anchor_seq)) ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:929:28: error: ‘it’ was not declared in this scope; did you mean ‘int’?
929 | if ( seqan::goDown(it, seqan::Dna5String(anchor_seq)) ) {
| ^~
| int
/<<PKGBUILDDIR>>/lib/alnread.cpp:929:32: error: ‘seqan’ has not been declared
929 | if ( seqan::goDown(it, seqan::Dna5String(anchor_seq)) ) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:935:23: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
935 | seed->vDesc = it.vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘void ReadAlignment::extend_alignment(char)’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:983:38: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
983 | auto last_vDesc = seeds.front()->vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: In lambda function:
/<<PKGBUILDDIR>>/lib/alnread.cpp:994:43: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
994 | bool is_duplicate = seed->vDesc == last_vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:995:36: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
995 | last_vDesc = seed->vDesc;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp: In member function ‘std::vector<unsigned char> ReadAlignment::getMAPQs() const’:
/<<PKGBUILDDIR>>/lib/alnread.cpp:1159:55: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
1159 | mapqFactorsSum += ( mapqFactor * ( s->vDesc.range.i2 - s->vDesc.range.i1 ) );
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:1159:75: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
1159 | mapqFactorsSum += ( mapqFactor * ( s->vDesc.range.i2 - s->vDesc.range.i1 ) );
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:1162:25: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
1162 | if ( s->vDesc.range.i2 - s->vDesc.range.i1 > 1 )
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:1162:45: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘vDesc’
1162 | if ( s->vDesc.range.i2 - s->vDesc.range.i1 > 1 )
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp: At global scope:
/<<PKGBUILDDIR>>/lib/alnread.cpp:1192:6: error: variable or field ‘addReadInfoToRecord’ declared void
1192 | void ReadAlignment::addReadInfoToRecord(seqan::BamAlignmentRecord & record) const {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnread.cpp:1192:41: error: ‘seqan’ has not been declared
1192 | void ReadAlignment::addReadInfoToRecord(seqan::BamAlignmentRecord & record) const {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnread.cpp:1192:69: error: ‘record’ was not declared in this scope
1192 | void ReadAlignment::addReadInfoToRecord(seqan::BamAlignmentRecord & record) const {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:53: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:78: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:91:34: error: ‘std::vector’ is not a type
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:91:40: error: expected ‘,’ or ‘...’ before ‘<’ token
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:91:14: error: ‘void Atomic_bfo::writeRecords(int)’ cannot be overloaded with ‘void Atomic_bfo::writeRecords(int)’
91 | void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:74:14: note: previous declaration ‘void Atomic_bfo::writeRecords(int)’
74 | void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: In constructor ‘Atomic_bfo::Atomic_bfo(std::string)’:
/<<PKGBUILDDIR>>/lib/alnout.h:49:43: error: class ‘Atomic_bfo’ does not have any field named ‘bfo’
49 | Atomic_bfo( std::string f_name) : bfo(f_name.c_str()) { }
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h: In member function ‘void Atomic_bfo::setContext(int)’:
/<<PKGBUILDDIR>>/lib/alnout.h:59:17: error: ‘bfo’ was not declared in this scope
59 | bfo.context = context;
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h:59:31: error: ‘context’ was not declared in this scope; did you mean ‘seqan2::context’?
59 | bfo.context = context;
| ^~~~~~~
| seqan2::context
In file included from /usr/include/seqan/stream.h:111,
from /usr/include/seqan/bam_io.h:49:
/usr/include/seqan/stream/formatted_file.h:866:1: note: ‘seqan2::context’ declared here
866 | context(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: In member function ‘void Atomic_bfo::writeHeader(int)’:
/<<PKGBUILDDIR>>/lib/alnout.h:67:17: error: ‘seqan’ has not been declared
67 | seqan::writeHeader( bfo, header );
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:67:37: error: ‘bfo’ was not declared in this scope
67 | seqan::writeHeader( bfo, header );
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h:67:42: error: ‘header’ was not declared in this scope
67 | seqan::writeHeader( bfo, header );
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: In member function ‘void Atomic_bfo::writeRecords(int)’:
/<<PKGBUILDDIR>>/lib/alnout.h:76:22: error: ‘records’ was not declared in this scope
76 | if ( records.size() == 0 )
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:81:17: error: ‘seqan’ has not been declared
81 | seqan::writeRecords(bfo, records);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:81:37: error: ‘bfo’ was not declared in this scope
81 | seqan::writeRecords(bfo, records);
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h:81:42: error: ‘records’ was not declared in this scope
81 | seqan::writeRecords(bfo, records);
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: In member function ‘void Atomic_bfo::writeRecords(int)’:
/<<PKGBUILDDIR>>/lib/alnout.h:93:22: error: ‘records’ was not declared in this scope
93 | if ( records.size() == 0 )
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:98:42: error: ‘records’ was not declared in this scope
98 | for ( auto & subvector : records)
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:99:25: error: ‘seqan’ has not been declared
99 | seqan::writeRecords(bfo, subvector);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:99:45: error: ‘bfo’ was not declared in this scope
99 | seqan::writeRecords(bfo, subvector);
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h: At global scope:
/<<PKGBUILDDIR>>/lib/alnout.h:118:9: error: ‘seqan’ does not name a type
118 | seqan::BamIOContext<seqan::StringSet<seqan::CharString> > context;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:119:9: error: ‘seqan’ does not name a type
119 | seqan::StringSet<seqan::CharString> refNames;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:120:9: error: ‘seqan’ does not name a type
120 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > refNamesCache;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: In member function ‘void BamFileOutDeque::set_context(std::vector<std::__cxx11::basic_string<char> >&, std::vector<unsigned int>&)’:
/<<PKGBUILDDIR>>/lib/alnout.h:130:17: error: ‘seqan’ has not been declared
130 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:130:39: error: ‘seqan’ has not been declared
130 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:130:56: error: ‘seqan’ has not been declared
130 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:130:75: error: expected primary-expression before ‘>’ token
130 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:130:81: error: ‘refNames’ was not declared in this scope; did you mean ‘rename’?
130 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
| ^~~~~~~~
| rename
/<<PKGBUILDDIR>>/lib/alnout.h:130:77: error: ‘rnc’ was not declared in this scope
130 | seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h:131:17: error: ‘refNamesCache’ was not declared in this scope
131 | refNamesCache = rnc;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:132:17: error: ‘seqan’ has not been declared
132 | seqan::BamIOContext<seqan::StringSet<seqan::CharString> > cxt(refNames, refNamesCache);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:132:37: error: ‘seqan’ has not been declared
132 | seqan::BamIOContext<seqan::StringSet<seqan::CharString> > cxt(refNames, refNamesCache);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:132:54: error: ‘seqan’ has not been declared
132 | seqan::BamIOContext<seqan::StringSet<seqan::CharString> > cxt(refNames, refNamesCache);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:132:73: error: expected primary-expression before ‘>’ token
132 | seqan::BamIOContext<seqan::StringSet<seqan::CharString> > cxt(refNames, refNamesCache);
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:132:75: error: ‘cxt’ was not declared in this scope
132 | seqan::BamIOContext<seqan::StringSet<seqan::CharString> > cxt(refNames, refNamesCache);
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.h:133:17: error: ‘context’ was not declared in this scope; did you mean ‘seqan2::context’?
133 | context = cxt;
| ^~~~~~~
| seqan2::context
/usr/include/seqan/stream/formatted_file.h:866:1: note: ‘seqan2::context’ declared here
866 | context(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:134:17: error: ‘seqan’ has not been declared
134 | seqan::contigNames(context) = seq_names;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:135:17: error: ‘seqan’ has not been declared
135 | seqan::contigLengths(context) = seq_lengths;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: In member function ‘void BamFileOutDeque::emplace_back(std::string)’:
/<<PKGBUILDDIR>>/lib/alnout.h:145:40: error: ‘context’ was not declared in this scope; did you mean ‘seqan2::context’?
145 | bfos.back().setContext(context);
| ^~~~~~~
| seqan2::context
/usr/include/seqan/stream/formatted_file.h:866:1: note: ‘seqan2::context’ declared here
866 | context(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
| ^~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h: At global scope:
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:74: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:249:30: error: ‘std::vector’ is not a type
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:249:36: error: expected ‘,’ or ‘...’ before ‘<’ token
249 | void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
| ^
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnstream.cpp: In member function ‘ReadAlignment* iAlnStream::get_alignment()’:
/<<PKGBUILDDIR>>/lib/alnstream.cpp:359:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
359 | fread(buffer.data(),1,buf_size,fstream);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnstream.cpp:389:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
389 | fread(buffer.data(),1,buf_size,fstream);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:166: CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o] Error 1
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:124: CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o] Error 1
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.h:257:36: error: ‘std::vector’ is not a type
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.h:257:42: error: expected ‘,’ or ‘...’ before ‘<’ token
257 | void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
| ^
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:180: CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o] Error 1
/<<PKGBUILDDIR>>/lib/alnout.cpp: In member function ‘void AlnOut::init()’:
/<<PKGBUILDDIR>>/lib/alnout.cpp:50:9: error: ‘seqan’ has not been declared
50 | seqan::BamHeader header = getBamHeader();
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:60:51: error: ‘header’ was not declared in this scope
60 | bfos[barcode].writeHeader(header);
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp: In member function ‘void AlnOut::__write_tile_to_bam__(Task)’:
/<<PKGBUILDDIR>>/lib/alnout.cpp:295:41: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
295 | std::vector<std::vector<seqan::BamAlignmentRecord>> mateRecords(mateAlignments.size(), std::vector<seqan::BamAlignmentRecord>(0));
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:295:66: error: template argument 1 is invalid
295 | std::vector<std::vector<seqan::BamAlignmentRecord>> mateRecords(mateAlignments.size(), std::vector<seqan::BamAlignmentRecord>(0));
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:295:66: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:295:145: error: template argument 1 is invalid
295 | std::vector<std::vector<seqan::BamAlignmentRecord>> mateRecords(mateAlignments.size(), std::vector<seqan::BamAlignmentRecord>(0));
| ^
/<<PKGBUILDDIR>>/lib/alnout.cpp:295:145: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:336:25: error: ‘seqan’ is not a class, namespace, or enumeration
336 | seqan::BamAlignmentRecord mate_record;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:337:25: error: ‘mate_record’ was not declared in this scope
337 | mate_record.qName = readname.str();
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:368:41: error: ‘mateRecords’ was not declared in this scope
368 | mateRecords[mateAlignmentIndex].push_back(mate_record);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:416:33: error: ‘seqan’ is not a class, namespace, or enumeration
416 | seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:416:47: error: ‘seqan’ is not a class, namespace, or enumeration
416 | seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:416:67: error: expected primary-expression before ‘>’ token
416 | seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
| ^
/<<PKGBUILDDIR>>/lib/alnout.cpp:416:69: error: expected primary-expression before ‘>’ token
416 | seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
| ^
/<<PKGBUILDDIR>>/lib/alnout.cpp:416:71: error: ‘cigar’ was not declared in this scope
416 | seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:416:86: error: ‘using std::__shared_ptr_access<Seed, __gnu_cxx::_S_atomic, false, false>::element_type = struct Seed’ {aka ‘struct Seed’} has no member named ‘returnSeqanCigarString’
416 | seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:38: error: ‘seqan’ is not a class, namespace, or enumeration
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:54: error: ‘seqan’ is not a class, namespace, or enumeration
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:68: error: ‘seqan’ is not a class, namespace, or enumeration
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:88: error: expected primary-expression before ‘>’ token
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:90: error: expected primary-expression before ‘>’ token
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:92: error: expected primary-expression before ‘>’ token
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:95: error: ‘::Type’ has not been declared
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:128: error: ‘elem’ was not declared in this scope
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:136: error: ‘end’ was not declared in this scope
428 | for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:428:136: note: suggested alternatives:
In file included from /usr/include/c++/14/string:53:
/usr/include/c++/14/bits/range_access.h:116:37: note: ‘std::end’
116 | template<typename _Tp> const _Tp* end(const valarray<_Tp>&) noexcept;
| ^~~
In file included from /usr/include/seqan/index/index_pizzachili.h:39,
from /usr/include/seqan/index.h:194,
from /<<PKGBUILDDIR>>/lib/kindex.h:9:
/usr/include/seqan/index/index_pizzachili_string.h:480:1: note: ‘seqan2::end’
480 | end(
| ^~~
In file included from /usr/include/boost/mpl/begin_end.hpp:17,
from /usr/include/boost/mpl/aux_/at_impl.hpp:17,
from /usr/include/boost/mpl/at.hpp:18,
from /usr/include/boost/multi_index_container.hpp:25,
from /usr/include/boost/property_tree/ptree.hpp:21,
from /usr/include/boost/property_tree/xml_parser.hpp:14,
from /<<PKGBUILDDIR>>/lib/headers.h:30:
/usr/include/boost/mpl/begin_end_fwd.hpp:23:38: note: ‘boost::mpl::end’
23 | template< typename Sequence > struct end;
| ^~~
In file included from /usr/include/boost/filesystem.hpp:18,
from /<<PKGBUILDDIR>>/lib/headers.h:29:
/usr/include/boost/filesystem/directory.hpp:1056:37: note: ‘boost::filesystem::end’
1056 | inline recursive_directory_iterator end(recursive_directory_iterator const&) BOOST_NOEXCEPT
| ^~~
In file included from /usr/include/boost/foreach.hpp:80,
from /<<PKGBUILDDIR>>/lib/headers.h:34:
/usr/include/boost/range/end.hpp:104:61: note: ‘boost::range_adl_barrier::end’
104 | inline BOOST_DEDUCED_TYPENAME range_iterator<const T>::type end( const T& r )
| ^~~
/usr/include/boost/foreach.hpp:736:1: note: ‘boost::foreach_detail_::end’
736 | end(auto_any_t, type2type<T *, C> *, boost::mpl::true_ *) // null-terminated C-style strings
| ^~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:467:41: error: ‘seqan’ is not a class, namespace, or enumeration
467 | seqan::BamAlignmentRecord record = mate_record;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:469:41: error: ‘record’ was not declared in this scope
469 | record.rID = CountType(p->gid / 2);
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:488:49: error: ‘seqan’ is not a class, namespace, or enumeration
488 | seqan::reverse(record.cigar);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:492:49: error: ‘seqan’ is not a class, namespace, or enumeration
492 | seqan::clear(record.seq);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:493:49: error: ‘seqan’ is not a class, namespace, or enumeration
493 | seqan::clear(record.qual);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:497:49: error: ‘seqan’ is not a class, namespace, or enumeration
497 | seqan::reverseComplement(record.seq);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:498:49: error: ‘seqan’ is not a class, namespace, or enumeration
498 | seqan::reverse(record.qual);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:503:41: error: ‘seqan’ is not a class, namespace, or enumeration
503 | seqan::BamTagsDict dict;
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:506:41: error: ‘seqan’ is not a class, namespace, or enumeration
506 | seqan::appendTagValue(dict, "AS", curr_seed_score);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:506:63: error: ‘dict’ was not declared in this scope
506 | seqan::appendTagValue(dict, "AS", curr_seed_score);
| ^~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:510:49: error: ‘seqan’ is not a class, namespace, or enumeration
510 | seqan::appendTagValue(dict, "BC", barcode);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:513:41: error: ‘seqan’ is not a class, namespace, or enumeration
513 | seqan::appendTagValue(dict, "NM", nm);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:519:41: error: ‘seqan’ is not a class, namespace, or enumeration
519 | seqan::appendTagValue(dict, "MD", mdz);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:521:55: error: ‘seqan’ is not a class, namespace, or enumeration
521 | record.tags = seqan::host(dict);
| ^~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:524:41: error: ‘mateRecords’ was not declared in this scope
524 | mateRecords[mateAlignmentIndex].push_back(record);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:538:38: error: ‘mateRecords’ was not declared in this scope
538 | if ( mateRecords[mateAlignmentIndex].size()==0 && globalAlignmentSettings.get_report_unmapped() ) {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:546:33: error: ‘mateRecords’ was not declared in this scope
546 | setMateSAMFlags(mateRecords);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp: At global scope:
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:6: error: variable or field ‘setMateSAMFlags’ declared void
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:55: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan2’?
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~
| seqan2
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 1 is invalid
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:80: error: template argument 2 is invalid
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:110: CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o] Error 1
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:85: error: ‘mateRecords’ was not declared in this scope
564 | void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:85: error: template argument 1 is invalid
/<<PKGBUILDDIR>>/lib/alnout.cpp:564:85: error: template argument 2 is invalid
make[3]: *** [CMakeFiles/HiLiveLibs.dir/build.make:138: CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:99: CMakeFiles/HiLiveLibs.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 -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-23T10:29:13Z
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: 2136
Build-Time: 12
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 36
Job: /tmp/debusine-fetch-exec-upload-cja7d46h/hilive_2.0a-4.dsc
Machine Architecture: arm64
Package: hilive
Package-Time: 78
Source-Version: 2.0a-4
Space: 2136
Status: attempted
Version: 2.0a-4
--------------------------------------------------------------------------------
Finished at 2024-11-23T10:29:13Z
Build needed 00:01:18, 2136k disk space