sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-09.freexian.com
+==============================================================================+
| porechop 0.2.4+dfsg-6 (arm64) Sat, 23 Nov 2024 10:27:59 +0000 |
+==============================================================================+
Package: porechop
Version: 0.2.4+dfsg-6
Source Version: 0.2.4+dfsg-6
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: binary
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/1053884/system.tar.xz to /tmp/tmp.sbuild.49H0g3v6WP...
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-utfv3ssy/seqan-apps-dbgsym_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-utfv3ssy/seqan-apps_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-utfv3ssy/libseqan2-dev_2.5.0~rc3+dfsg-1_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/porechop-p78GLt/resolver-eW3YlY' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ InRelease
Ign:1 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ InRelease
Get:2 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ Release [606 B]
Get:2 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ Release [606 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:4 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ Release.gpg
Ign:4 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ Release.gpg
Get:5 file:/build/porechop-p78GLt/resolver-HQ4tuk/apt_archive ./ Packages [4687 B]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9958 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4913 kB]
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
apt base-files libapt-pkg6.0t64 libxml-sax-perl
4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2411 kB of archives.
After this operation, 206 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 base-files arm64 13.6 [72.9 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.14 [969 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.14 [1316 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../libxml-sax-perl_1.02+dfsg-4_all.deb ...
Unpacking libxml-sax-perl (1.02+dfsg-4) over (1.02+dfsg-3) ...
Setting up libxml-sax-perl (1.02+dfsg-4) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-3) ...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/tmp/debusine-fetch-exec-upload-utfv3ssy/porechop_0.2.4+dfsg-6.dsc exists in /tmp/debusine-fetch-exec-upload-utfv3ssy; copying to chroot
I: NOTICE: Log filtering will replace 'build/porechop-p78GLt/porechop-0.2.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/porechop-p78GLt' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [708 B]
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Reading package lists...
Ign:1 file:/<<BUILDDIR>>/resolver-HQ4tuk/apt_archive ./ InRelease
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Get:2 file:/<<BUILDDIR>>/resolver-HQ4tuk/apt_archive ./ Release [606 B]
Ign:3 file:/<<BUILDDIR>>/resolver-HQ4tuk/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 cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper dh-autoreconf
dh-python dh-strip-nondeterminism dwz fakeroot g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libc-dev-bin
libc6-dev libcc1-0 libcrypt-dev libdebhelper-perl libelf1t64 libexpat1
libexpat1-dev libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev
libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore
liblsan0 libmpc3 libmpfr6 libncursesw6 libnsl2 libpython3-dev
libpython3-stdlib libpython3.12-dev libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 libseqan2-dev libstdc++-14-dev
libtirpc-common libtirpc3t64 libtool libtsan2 libubsan1 linux-libc-dev m4
media-types po-debconf python3 python3-autocommand python3-dev
python3-inflect python3-jaraco.context python3-jaraco.functools
python3-jaraco.text python3-minimal python3-more-itertools
python3-pkg-resources python3-setuptools python3-typeguard
python3-typing-extensions python3-zipp python3.12 python3.12-dev
python3.12-minimal rpcsvc-proto zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales
cpp-14-doc dh-make flit python3-build python3-installer python3-wheel
gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
gdb-aarch64-linux-gnu libc-devtools glibc-doc libstdc++-14-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3-doc
python3-tk python3-venv python-setuptools-doc python3.12-venv python3.12-doc
binfmt-support
Recommended packages:
manpages manpages-dev libarchive-cpio-perl javascript-common libgpm2
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper dh-autoreconf
dh-python dh-strip-nondeterminism dwz fakeroot g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libc-dev-bin
libc6-dev libcc1-0 libcrypt-dev libdebhelper-perl libelf1t64 libexpat1
libexpat1-dev libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev
libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore
liblsan0 libmpc3 libmpfr6 libncursesw6 libnsl2 libpython3-dev
libpython3-stdlib libpython3.12-dev libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 libseqan2-dev libstdc++-14-dev
libtirpc-common libtirpc3t64 libtool libtsan2 libubsan1 linux-libc-dev m4
media-types po-debconf python3 python3-autocommand python3-dev
python3-inflect python3-jaraco.context python3-jaraco.functools
python3-jaraco.text python3-minimal python3-more-itertools
python3-pkg-resources python3-setuptools python3-typeguard
python3-typing-extensions python3-zipp python3.12 python3.12-dev
python3.12-minimal rpcsvc-proto sbuild-build-depends-main-dummy zlib1g-dev
0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded.
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Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B]
Get:3 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB]
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Get:50 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:51 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
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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 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:66 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 75.2.0-1 [731 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20241024 [109 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 libpython3-dev arm64 3.12.7-1 [9980 B]
Get:82 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 python3-dev arm64 3.12.7-1 [26.1 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 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-python_6.20241024 dh-strip-nondeterminism_1.14.0-1 diffstat_1.67-1 diffutils_1:3.10-1+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-8 g++-14-aarch64-linux-gnu_14.2.0-8 g++-aarch64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-8 gcc-14-aarch64-linux-gnu_14.2.0-8 gcc-14-base_14.2.0-8 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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: porechop
Binary: porechop
Architecture: any
Version: 0.2.4+dfsg-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Cédric Lood <cedric.lood@kuleuven.be>, Andreas Tille <tille@debian.org>
Homepage: https://rrwick.github.io/Porechop
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/porechop
Vcs-Git: https://salsa.debian.org/med-team/porechop.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools
Package-List:
porechop deb science optional arch=any
Checksums-Sha1:
ca42641ad185404433d21282554185aa184bf437 726312 porechop_0.2.4+dfsg.orig.tar.xz
bb290af32705362aa5ff264977de724eab70f86e 6152 porechop_0.2.4+dfsg-6.debian.tar.xz
Checksums-Sha256:
6d018c3c39777b36697cb1182ecaac9f981ee78c3660347fb83e52351cd79a2c 726312 porechop_0.2.4+dfsg.orig.tar.xz
4adf0600768b96d2efc1cda4c87031d01b09796b8da7cd09ccde621d3bd34807 6152 porechop_0.2.4+dfsg-6.debian.tar.xz
Files:
a09d363d707181eb1013200716142ad7 726312 porechop_0.2.4+dfsg.orig.tar.xz
81be161a3f63d898d8cbf0fab2d09398 6152 porechop_0.2.4+dfsg-6.debian.tar.xz
Dgit: 34a1fd15de707d4b2e997798036702b1f8a39647 debian archive/debian/0.2.4+dfsg-6 https://git.dgit.debian.org/porechop
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gpgv: Signature made Fri Jul 12 21:53:00 2024 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-6.dsc: no acceptable signature found
dpkg-source: info: extracting porechop in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking porechop_0.2.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking porechop_0.2.4+dfsg-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add_python_interpreter_line.patch
dpkg-source: info: applying no_soname.patch
dpkg-source: info: applying define-all-attribute-in-clean.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 porechop
dpkg-buildpackage: info: source version 0.2.4+dfsg-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --with python3 --buildsystem pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py clean
running clean
Deleting directory: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
dh_autoreconf_clean -O--buildsystem=pybuild
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
# Removing left .so files.
find . -name "*.so" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary
dh binary --with python3 --buildsystem pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/porechop.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/adapters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/misc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/cpp_function_wrappers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
copying porechop/nanopore_read.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop
Cleaning previous compilation: make clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f porechop/src/alignment.o porechop/src/adapter_align.o
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
Compiling Porechop: make -j 4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o porechop/src/alignment.o porechop/src/alignment.cpp
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp
In file included from /usr/include/seqan/align.h:151,
from porechop/include/alignment.h:8,
from porechop/src/alignment.cpp:2:
/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 porechop/include/alignment.h:8,
from porechop/include/adapter_align.h:7,
from porechop/src/adapter_align.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>>
| ^~
porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
10 | using namespace seqan;
| ^~~~~
porechop/include/alignment.h:15:26: error: expected ‘)’ before ‘<’ token
15 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ~ ^
| )
porechop/src/alignment.cpp:6:33: error: expected constructor, destructor, or type conversion before ‘(’ token
6 | ScoredAlignment::ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ^
porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
10 | using namespace seqan;
| ^~~~~
porechop/include/alignment.h:15:26: error: expected ‘)’ before ‘<’ token
15 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ~ ^
| )
porechop/include/adapter_align.h:9:17: error: ‘seqan’ is not a namespace-name
9 | using namespace seqan;
| ^~~~~
porechop/src/adapter_align.cpp: In function ‘char* adapterAlignment(char*, char*, int, int, int, int)’:
porechop/src/adapter_align.cpp:15:5: error: ‘Dna5String’ was not declared in this scope; did you mean ‘seqan2::Dna5String’?
15 | Dna5String sequenceH = readSeq;
| ^~~~~~~~~~
| seqan2::Dna5String
In file included from /usr/include/seqan/sequence.h:112,
from porechop/include/adapter_align.h:4:
/usr/include/seqan/sequence/sequence_shortcuts.h:119:36: note: ‘seqan2::Dna5String’ declared here
119 | typedef String<Dna5, Alloc<void> > Dna5String;
| ^~~~~~~~~~
porechop/src/adapter_align.cpp:16:15: error: expected ‘;’ before ‘sequenceV’
16 | Dna5String sequenceV = adapterSeq;
| ^~~~~~~~~~
| ;
porechop/src/adapter_align.cpp:20:5: error: ‘Align’ was not declared in this scope; did you mean ‘seqan2::Align’?
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~
| seqan2::Align
In file included from /usr/include/seqan/file.h:65,
from /usr/include/seqan/stream.h:62,
from /usr/include/seqan/score.h:43,
from /usr/include/seqan/graph_align.h:45,
from /usr/include/seqan/align.h:59:
/usr/include/seqan/file/file_forwards.h:46:7: note: ‘seqan2::Align’ declared here
46 | class Align;
| ^~~~~
porechop/src/adapter_align.cpp:20:23: error: ‘ArrayGaps’ was not declared in this scope; did you mean ‘seqan2::ArrayGaps’?
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~~~~~
| seqan2::ArrayGaps
In file included from /usr/include/seqan/align.h:85:
/usr/include/seqan/align/gaps_array.h:75:25: note: ‘seqan2::ArrayGaps’ declared here
75 | typedef Tag<ArrayGaps_> ArrayGaps;
| ^~~~~~~~~
porechop/src/adapter_align.cpp:20:34: error: ‘alignment’ was not declared in this scope
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~~~~~
porechop/src/adapter_align.cpp:21:12: error: ‘rows’ was not declared in this scope; did you mean ‘seqan2::rows’?
21 | resize(rows(alignment), 2);
| ^~~~
| seqan2::rows
In file included from /usr/include/seqan/align.h:97:
/usr/include/seqan/align/align_base.h:341:1: note: ‘seqan2::rows’ declared here
341 | rows(Align<TSource, TSpec> const & me)
| ^~~~
porechop/src/adapter_align.cpp:21:5: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
21 | resize(rows(alignment), 2);
| ^~~~~~
| seqan2::resize
In file included from /usr/include/seqan/align.h:146:
/usr/include/seqan/align/dp_matrix_sparse.h:95:1: note: ‘seqan2::resize’ declared here
95 | resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
| ^~~~~~
porechop/src/adapter_align.cpp:22:18: error: ‘row’ was not declared in this scope; did you mean ‘seqan2::row’?
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~
| seqan2::row
/usr/include/seqan/align/align_base.h:372:1: note: ‘seqan2::row’ declared here
372 | row(Align<TSource, TSpec> const & me,
| ^~~
porechop/src/adapter_align.cpp:22:37: error: ‘sequenceH’ was not declared in this scope
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~~~~~~~
porechop/src/adapter_align.cpp:22:5: error: ‘assignSource’ was not declared in this scope; did you mean ‘seqan2::assignSource’?
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~~~~~~~~~~
| seqan2::assignSource
In file included from /usr/include/seqan/align.h:89:
/usr/include/seqan/align/gaps_anchor.h:672:1: note: ‘seqan2::assignSource’ declared here
672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source)
| ^~~~~~~~~~~~
porechop/src/adapter_align.cpp:23:37: error: ‘sequenceV’ was not declared in this scope
23 | assignSource(row(alignment, 1), sequenceV);
| ^~~~~~~~~
porechop/src/adapter_align.cpp:24:5: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
24 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore);
| ^~~~~
| seqan2::Score
In file included from /usr/include/seqan/score.h:45:
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
porechop/src/adapter_align.cpp:24:11: error: expected primary-expression before ‘int’
24 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore);
| ^~~
porechop/src/adapter_align.cpp:26:5: error: ‘AlignConfig’ was not declared in this scope; did you mean ‘seqan2::AlignConfig’?
26 | AlignConfig<true, true, true, true> alignConfig;
| ^~~~~~~~~~~
| seqan2::AlignConfig
In file included from /usr/include/seqan/align.h:70:
/usr/include/seqan/align/align_config.h:93:7: note: ‘seqan2::AlignConfig’ declared here
93 | class AlignConfig
| ^~~~~~~~~~~
porechop/src/adapter_align.cpp:26:41: error: ‘alignConfig’ was not declared in this scope
26 | AlignConfig<true, true, true, true> alignConfig;
| ^~~~~~~~~~~
porechop/src/adapter_align.cpp:27:44: error: ‘scoringScheme’ was not declared in this scope
27 | int score = globalAlignment(alignment, scoringScheme, alignConfig);
| ^~~~~~~~~~~~~
porechop/src/adapter_align.cpp:27:17: error: ‘globalAlignment’ was not declared in this scope; did you mean ‘seqan2::globalAlignment’?
27 | int score = globalAlignment(alignment, scoringScheme, alignConfig);
| ^~~~~~~~~~~~~~~
| seqan2::globalAlignment
In file included from /usr/include/seqan/align.h:218:
/usr/include/seqan/align/global_alignment_specialized.h:121:5: note: ‘seqan2::globalAlignment’ declared here
121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
| ^~~~~~~~~~~~~~~
porechop/src/adapter_align.cpp:29:48: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
29 | ScoredAlignment scoredAlignment(alignment, length(readSeq), length(adapterSeq), score);
| ^~~~~~
| seqan2::length
In file included from /usr/include/seqan/align.h:145:
/usr/include/seqan/align/dp_matrix.h:419:1: note: ‘seqan2::length’ declared here
419 | length(DPMatrix_<TValue, TMatrixSpec, THost> const & dpMatrix)
| ^~~~~~
make[1]: *** [Makefile:56: porechop/src/alignment.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [Makefile:56: porechop/src/adapter_align.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -O--buildsystem=pybuild
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install --destdir=debian/porechop/ -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/porechop
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
Cleaning previous compilation: make clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f porechop/src/alignment.o porechop/src/adapter_align.o
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
Compiling Porechop: make -j 4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o porechop/src/alignment.o porechop/src/alignment.cpp
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp
In file included from /usr/include/seqan/align.h:151,
from porechop/include/alignment.h:8,
from porechop/src/alignment.cpp:2:
/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 porechop/include/alignment.h:8,
from porechop/include/adapter_align.h:7,
from porechop/src/adapter_align.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>>
| ^~
porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
10 | using namespace seqan;
| ^~~~~
porechop/include/alignment.h:15:26: error: expected ‘)’ before ‘<’ token
15 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ~ ^
| )
porechop/src/alignment.cpp:6:33: error: expected constructor, destructor, or type conversion before ‘(’ token
6 | ScoredAlignment::ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ^
porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
10 | using namespace seqan;
| ^~~~~
porechop/include/alignment.h:15:26: error: expected ‘)’ before ‘<’ token
15 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ~ ^
| )
porechop/include/adapter_align.h:9:17: error: ‘seqan’ is not a namespace-name
9 | using namespace seqan;
| ^~~~~
porechop/src/adapter_align.cpp: In function ‘char* adapterAlignment(char*, char*, int, int, int, int)’:
porechop/src/adapter_align.cpp:15:5: error: ‘Dna5String’ was not declared in this scope; did you mean ‘seqan2::Dna5String’?
15 | Dna5String sequenceH = readSeq;
| ^~~~~~~~~~
| seqan2::Dna5String
In file included from /usr/include/seqan/sequence.h:112,
from porechop/include/adapter_align.h:4:
/usr/include/seqan/sequence/sequence_shortcuts.h:119:36: note: ‘seqan2::Dna5String’ declared here
119 | typedef String<Dna5, Alloc<void> > Dna5String;
| ^~~~~~~~~~
porechop/src/adapter_align.cpp:16:15: error: expected ‘;’ before ‘sequenceV’
16 | Dna5String sequenceV = adapterSeq;
| ^~~~~~~~~~
| ;
porechop/src/adapter_align.cpp:20:5: error: ‘Align’ was not declared in this scope; did you mean ‘seqan2::Align’?
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~
| seqan2::Align
In file included from /usr/include/seqan/file.h:65,
from /usr/include/seqan/stream.h:62,
from /usr/include/seqan/score.h:43,
from /usr/include/seqan/graph_align.h:45,
from /usr/include/seqan/align.h:59:
/usr/include/seqan/file/file_forwards.h:46:7: note: ‘seqan2::Align’ declared here
46 | class Align;
| ^~~~~
porechop/src/adapter_align.cpp:20:23: error: ‘ArrayGaps’ was not declared in this scope; did you mean ‘seqan2::ArrayGaps’?
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~~~~~
| seqan2::ArrayGaps
In file included from /usr/include/seqan/align.h:85:
/usr/include/seqan/align/gaps_array.h:75:25: note: ‘seqan2::ArrayGaps’ declared here
75 | typedef Tag<ArrayGaps_> ArrayGaps;
| ^~~~~~~~~
porechop/src/adapter_align.cpp:20:34: error: ‘alignment’ was not declared in this scope
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~~~~~
porechop/src/adapter_align.cpp:21:12: error: ‘rows’ was not declared in this scope; did you mean ‘seqan2::rows’?
21 | resize(rows(alignment), 2);
| ^~~~
| seqan2::rows
In file included from /usr/include/seqan/align.h:97:
/usr/include/seqan/align/align_base.h:341:1: note: ‘seqan2::rows’ declared here
341 | rows(Align<TSource, TSpec> const & me)
| ^~~~
porechop/src/adapter_align.cpp:21:5: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
21 | resize(rows(alignment), 2);
| ^~~~~~
| seqan2::resize
In file included from /usr/include/seqan/align.h:146:
/usr/include/seqan/align/dp_matrix_sparse.h:95:1: note: ‘seqan2::resize’ declared here
95 | resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
| ^~~~~~
porechop/src/adapter_align.cpp:22:18: error: ‘row’ was not declared in this scope; did you mean ‘seqan2::row’?
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~
| seqan2::row
/usr/include/seqan/align/align_base.h:372:1: note: ‘seqan2::row’ declared here
372 | row(Align<TSource, TSpec> const & me,
| ^~~
porechop/src/adapter_align.cpp:22:37: error: ‘sequenceH’ was not declared in this scope
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~~~~~~~
porechop/src/adapter_align.cpp:22:5: error: ‘assignSource’ was not declared in this scope; did you mean ‘seqan2::assignSource’?
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~~~~~~~~~~
| seqan2::assignSource
In file included from /usr/include/seqan/align.h:89:
/usr/include/seqan/align/gaps_anchor.h:672:1: note: ‘seqan2::assignSource’ declared here
672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source)
| ^~~~~~~~~~~~
porechop/src/adapter_align.cpp:23:37: error: ‘sequenceV’ was not declared in this scope
23 | assignSource(row(alignment, 1), sequenceV);
| ^~~~~~~~~
porechop/src/adapter_align.cpp:24:5: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
24 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore);
| ^~~~~
| seqan2::Score
In file included from /usr/include/seqan/score.h:45:
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
porechop/src/adapter_align.cpp:24:11: error: expected primary-expression before ‘int’
24 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore);
| ^~~
porechop/src/adapter_align.cpp:26:5: error: ‘AlignConfig’ was not declared in this scope; did you mean ‘seqan2::AlignConfig’?
26 | AlignConfig<true, true, true, true> alignConfig;
| ^~~~~~~~~~~
| seqan2::AlignConfig
In file included from /usr/include/seqan/align.h:70:
/usr/include/seqan/align/align_config.h:93:7: note: ‘seqan2::AlignConfig’ declared here
93 | class AlignConfig
| ^~~~~~~~~~~
porechop/src/adapter_align.cpp:26:41: error: ‘alignConfig’ was not declared in this scope
26 | AlignConfig<true, true, true, true> alignConfig;
| ^~~~~~~~~~~
porechop/src/adapter_align.cpp:27:44: error: ‘scoringScheme’ was not declared in this scope
27 | int score = globalAlignment(alignment, scoringScheme, alignConfig);
| ^~~~~~~~~~~~~
porechop/src/adapter_align.cpp:27:17: error: ‘globalAlignment’ was not declared in this scope; did you mean ‘seqan2::globalAlignment’?
27 | int score = globalAlignment(alignment, scoringScheme, alignConfig);
| ^~~~~~~~~~~~~~~
| seqan2::globalAlignment
In file included from /usr/include/seqan/align.h:218:
/usr/include/seqan/align/global_alignment_specialized.h:121:5: note: ‘seqan2::globalAlignment’ declared here
121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
| ^~~~~~~~~~~~~~~
porechop/src/adapter_align.cpp:29:48: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
29 | ScoredAlignment scoredAlignment(alignment, length(readSeq), length(adapterSeq), score);
| ^~~~~~
| seqan2::length
In file included from /usr/include/seqan/align.h:145:
/usr/include/seqan/align/dp_matrix.h:419:1: note: ‘seqan2::length’ declared here
419 | length(DPMatrix_<TValue, TMatrixSpec, THost> const & dpMatrix)
| ^~~~~~
make[1]: *** [Makefile:56: porechop/src/alignment.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [Makefile:56: porechop/src/adapter_align.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
running install_lib
creating /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages
creating /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/version.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/porechop.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/__init__.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/adapters.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/misc.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/cpp_function_wrappers.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/porechop/nanopore_read.py -> /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/version.py to version.cpython-312.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/porechop.py to porechop.cpython-312.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/__init__.py to __init__.cpython-312.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/adapters.py to adapters.cpython-312.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/misc.py to misc.cpython-312.pyc
/usr/lib/python3.12/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\['
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-312.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop/nanopore_read.py to nanopore_read.cpython-312.pyc
running install_egg_info
running egg_info
creating porechop.egg-info
writing porechop.egg-info/PKG-INFO
writing dependency_links to porechop.egg-info/dependency_links.txt
writing entry points to porechop.egg-info/entry_points.txt
writing top-level names to porechop.egg-info/top_level.txt
writing manifest file 'porechop.egg-info/SOURCES.txt'
reading manifest file 'porechop.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'porechop.egg-info/SOURCES.txt'
Copying porechop.egg-info to /<<PKGBUILDDIR>>/debian/porechop/usr/lib/python3.12/dist-packages/porechop-0.2.4.egg-info
Skipping SOURCES.txt
running install_scripts
Installing porechop script to /<<PKGBUILDDIR>>/debian/porechop/usr/bin
error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so'
E: pybuild pybuild:389: install: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/porechop
dh_auto_install: error: pybuild --install -i python{version} -p 3.12 --dest-dir /<<BUILDDIR>>/porechop-0.2.4\+dfsg/debian/porechop returned exit code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-23T10:29:11Z
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: 2744
Build-Time: 10
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 31
Job: /tmp/debusine-fetch-exec-upload-utfv3ssy/porechop_0.2.4+dfsg-6.dsc
Machine Architecture: arm64
Package: porechop
Package-Time: 72
Source-Version: 0.2.4+dfsg-6
Space: 2744
Status: attempted
Version: 0.2.4+dfsg-6
--------------------------------------------------------------------------------
Finished at 2024-11-23T10:29:11Z
Build needed 00:01:12, 2744k disk space