python-pysam →
0.21.0+ds-1 →
armhf → 2023-09-22 23:14:43
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| python-pysam 0.21.0+ds-1 (armhf) Fri, 22 Sep 2023 22:52:27 +0000 |
+==============================================================================+
Package: python-pysam
Version: 0.21.0+ds-1
Source Version: 0.21.0+ds-1
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-1826ff9b-1457-46db-b4ec-798a66329913' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-zalcIO/resolver-jFbpbj' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.6 MB]
Fetched 28.7 MB in 11s (2579 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-pysam.git
Please use:
git clone https://salsa.debian.org/med-team/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1469 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main python-pysam 0.21.0+ds-1 (dsc) [2562 B]
Get:2 http://172.17.4.1/private trixie-staging/main python-pysam 0.21.0+ds-1 (tar) [1455 kB]
Get:3 http://172.17.4.1/private trixie-staging/main python-pysam 0.21.0+ds-1 (diff) [10.5 kB]
Fetched 1469 kB in 0s (5443 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-zalcIO/python-pysam-0.21.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-zalcIO' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
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Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
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Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3
debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
libjs-jquery libjs-sphinxdoc libjs-underscore liblzma-dev libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev
libpython3.11-minimal libpython3.11-stdlib librtmp1 libssh2-1
libsub-override-perl libtool libuchardet0 libunistring5 libxml2 m4 man-db
media-types po-debconf python3 python3-all python3-all-dev python3-dev
python3-distutils python3-iniconfig python3-lib2to3 python3-minimal
python3-packaging python3-pkg-resources python3-pluggy python3-pytest
python3-setuptools python3.11 python3.11-dev python3.11-minimal samtools
tabix zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib
texlive-latex-recommended cython-doc dh-make flit python3-build
python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev
groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc
python3.11-venv python3.11-doc binfmt-support cwltool
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl python3-pygments
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3
debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
libjs-jquery libjs-sphinxdoc libjs-underscore liblzma-dev libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev
libpython3.11-minimal libpython3.11-stdlib librtmp1 libssh2-1
libsub-override-perl libtool libuchardet0 libunistring5 libxml2 m4 man-db
media-types po-debconf python3 python3-all python3-all-dev python3-dev
python3-distutils python3-iniconfig python3-lib2to3 python3-minimal
python3-packaging python3-pkg-resources python3-pluggy python3-pytest
python3-setuptools python3.11 python3.11-dev python3.11-minimal samtools
sbuild-build-depends-main-dummy tabix zlib1g-dev
0 upgraded, 81 newly installed, 0 to remove and 12 not upgraded.
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Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.6.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.1 bash_5.2.15-2 bcftools_1.13-1 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 cython3_0.29.36-1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.6 debianutils_5.13 dh-autoreconf_20 dh-exec_0.27+b1 dh-python_6.20230825 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-12 gettext-base_0.21-12 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-3 libacl1_2.3.1-3 libapt-pkg6.0_2.6.1 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.6-1 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.40-2+rpi2 libblkid1_2.39.2-1 libbrotli1_1.0.9-2+b3 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-9+rpi1+deb12u1 libc-dev-bin_2.36-9+rpi1+deb12u1 libc6_2.36-9+rpi1+deb12u1 libc6-dev_2.36-9+rpi1+deb12u1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_12.2.0-14+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.40-2+rpi2 libctf0_2.40-2+rpi2 libcurl3-gnutls_7.88.1-10+rpi1 libcurl4-gnutls-dev_7.88.1-10+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270 libdebhelper-perl_13.11.6 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.21.22+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libexpat1-dev_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14+rpi1 libgcc-s1_12.2.0-14+rpi1 libgcrypt20_1.10.2-2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.7.9-2 libgomp1_12.2.0-14+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-3 libhogweed6_3.9.1-2 libhts-dev_1.17+ds-1 libhts3_1.17+ds-1 libhtscodecs2_1.5.1-1 libicu72_72.1-3 libidn2-0_2.3.3-1+b2 libisl23_0.26-3 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_5.3.0-7 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.20.1-3 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-3 libkrb5support0_1.20.1-3 libksba8_1.6.3-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.4-0.1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncurses6_6.4+20230625-2 libncursesw6_6.4+20230625-2 libnettle8_3.9.1-2 libnghttp2-14_1.56.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-7 libpam-modules-bin_1.5.2-7 libpam-runtime_1.5.2-7 libpam0g_1.5.2-7 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.32_5.32.1-6 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libpython3-all-dev_3.11.4-5 libpython3-dev_3.11.4-5 libpython3-stdlib_3.11.4-5 libpython3.11_3.11.5-3 libpython3.11-dev_3.11.5-3 libpython3.11-minimal_3.11.5-3 libpython3.11-stdlib_3.11.5-3 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.4-1+b2 libsepol1_3.1-1 libsepol2_3.5-1 libsmartcols1_2.39.2-1 libsqlite3-0_3.43.1-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl1.1_1.1.1o-1 libssl3_3.0.10-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-1 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.2-1 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.32_5.32.1-6 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-all_3.11.4-5 python3-all-dev_3.11.4-5 python3-dev_3.11.4-5 python3-distutils_3.11.5-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.11.5-1 python3-minimal_3.11.4-5 python3-packaging_23.1-1 python3-pkg-resources_68.1.2-1 python3-pluggy_1.3.0-1 python3-pytest_7.4.2-1 python3-setuptools_68.1.2-1 python3.11_3.11.5-3 python3.11-dev_3.11.5-3 python3.11-minimal_3.11.5-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 samtools_1.17-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.07-1 tabix_1.17+ds-1 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_37 util-linux_2.39.2-1 util-linux-extra_2.39.2-1 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: python-pysam
Binary: python3-pysam, python-pysam-tests
Architecture: any all
Version: 0.21.0+ds-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://pysam.readthedocs.org/en/latest
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
Testsuite: autopkgtest, autopkgtest-pkg-python
Testsuite-Triggers: @builddeps@
Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix <!nocheck>, samtools <!nocheck>, bcftools <!nocheck>, python3-pytest <!nocheck>
Package-List:
python-pysam-tests deb python optional arch=all
python3-pysam deb python optional arch=any
Checksums-Sha1:
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40dd6caa92ddc27654906ee313b533d8b49d37c8 10548 python-pysam_0.21.0+ds-1.debian.tar.xz
Checksums-Sha256:
d6126717f11e261ba3ad1fa683cf038f0af044b2c2efbf9be68ec7f8f5e791b5 1455428 python-pysam_0.21.0+ds.orig.tar.xz
26d33fcda34360d10473f77fcb16db55d5f3122392d37d0350cb776d2ede7ca3 10548 python-pysam_0.21.0+ds-1.debian.tar.xz
Files:
3ac021fcf33679ba6bfc7c5ea2207056 1455428 python-pysam_0.21.0+ds.orig.tar.xz
646650ec643a2782c476fb05234468e8 10548 python-pysam_0.21.0+ds-1.debian.tar.xz
Dgit: ebbf869260bc7f7f6f6b59d89c091bf85533ccec debian archive/debian/0.21.0+ds-1 https://git.dgit.debian.org/python-pysam
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gpgv: Signature made Fri Jun 23 18:26:02 2023 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 ./python-pysam_0.21.0+ds-1.dsc: no acceptable signature found
dpkg-source: info: extracting python-pysam in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-pysam_0.21.0+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.21.0+ds-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_remote.patch
dpkg-source: info: applying clean_less
dpkg-source: info: applying skip-test-on-32-bit.patch
dpkg-source: info: applying typos.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=cb0b5f3cf8de40c08a0d7553ac14d2c6
JOURNAL_STREAM=8:37174
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-1826ff9b-1457-46db-b4ec-798a66329913
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c16669
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.21.0+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<PKGBUILDDIR>>/tests/pysam_data'
rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \
all.stamp *~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
rm -f all.stamp *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*.bam" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "pysam_uncompressed.bam" -delete
rm -rf tests/pysam_test_work \
tests/example_htslib.gtf.gz.tbi \
tests/log.txt \
tests/test.bam \
tests/_compile_test.c \
tests/pysam_ex2.sam \
tests/__pycache__ \
pysam/calignmentfile.c \
pysam/cbcf.c \
tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
tests/pysam_data/ex1.fa.gz \
tests/pysam_data/ex1.fa.gz.gzi \
tests/pysam_data/ex1_csi.bam.csi
rm -rf .pytest_cache/
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:291: python3.11 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
rm -f \
pysam/config.py \
pysam/config.h \
pysam/lib*.c \
samtools/config.h \
bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:291: python3.11 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:291: /usr/bin/python3 setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/Pileup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/bcftools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/samtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing requirements to pysam.egg-info/requires.txt
writing top-level names to pysam.egg-info/top_level.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'pysam/libc*.c'
warning: no files found matching 'win32/*.[ch]'
warning: no files found matching 'htslib/LICENSE'
warning: no files found matching 'htslib/README'
warning: no files found matching '*.[ch]' under directory 'htslib'
warning: no previously-included files found matching 'htslib/*config*.h'
warning: no files found matching 'htslib/configure.ac'
warning: no files found matching 'htslib/m4/*.m4'
warning: no files found matching 'htslib/*.in'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/version.sh'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/*.mk'
warning: no previously-included files found matching 'htslib/config.mk'
warning: no previously-included files found matching 'htslib/htscodecs.mk'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pysam.include.samtools.lz4' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pysam.include.samtools.lz4' to be distributed and are
already explicitly excluding 'pysam.include.samtools.lz4' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying pysam/cbcftools_util.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/htslib_util.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/htslib_util.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignedsegment.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignedsegment.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignmentfile.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignmentfile.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcf.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcf.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcftools.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcftools.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbgzf.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbgzf.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcfaidx.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcfaidx.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libchtslib.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libchtslib.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamfile.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamfile.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamtools.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamtools.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabix.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabix.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabixproxies.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabixproxies.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcutils.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcutils.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcvcf.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcvcf.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/py.typed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/pysam_util.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/pysam_util.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/version.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/version.pyi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam
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copying samtools/LICENSE -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
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copying samtools/bam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/bam.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
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copying bcftools/bam2bcf_indel.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf_indel.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bin.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bin.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/ccall.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/ccall.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/cigar_state.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/cols.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/cols.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/consensus.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/consensus.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/convert.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/convert.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/csq.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/csq.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/dbuf.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/dist.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/dist.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/dist.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/em.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/em.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/extsort.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/extsort.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/extsort.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/filter.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/filter.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/hclust.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/hclust.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/kmin.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/kmin.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/main.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/main.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/mcall.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/mcall.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/mpileup.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/mpileup.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/prob1.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/prob1.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/read_consensus.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/read_consensus.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/read_consensus.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/regidx.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/regidx.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/reheader.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/reheader.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/str_finder.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/str_finder.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/str_finder.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/tabix.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/tabix.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/utlist.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfannotate.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfannotate.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfcall.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfcall.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfcnv.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfcnv.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfconcat.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfconcat.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfconvert.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfconvert.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcffilter.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcffilter.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfgtcheck.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfgtcheck.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfhead.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfhead.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfindex.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfindex.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfisec.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfisec.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfmerge.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfmerge.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfnorm.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfnorm.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfplugin.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfplugin.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfquery.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfquery.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfroh.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfroh.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfsom.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfsom.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfsort.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfsort.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfstats.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfstats.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfview.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfview.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/version.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/version.c.pysam.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/version.sh -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
cythoning pysam/libcutils.pyx to pysam/libcutils.c
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2582:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2631:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
cythoning pysam/libctabix.pyx to pysam/libctabix.c
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armv7l-cpython-311
creating build/temp.linux-armv7l-cpython-311/pysam
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/htslib_util.c -o build/temp.linux-armv7l-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libchtslib.c -o build/temp.linux-armv7l-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/htslib_util.o build/temp.linux-armv7l-cpython-311/pysam/libchtslib.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating build/temp.linux-armv7l-cpython-311/samtools
creating build/temp.linux-armv7l-cpython-311/samtools/lz4
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/cram_size.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/cram_size.c.pysam.c: In function ‘cram_size’:
samtools/cram_size.c.pysam.c:563:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=]
563 | fprintf(outfp, "Total file size %18"PRId64"\n", end);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~
| |
| off_t {aka long int}
In file included from /usr/include/htslib/hts.h:33,
from /usr/include/htslib/sam.h:33,
from samtools/cram_size.c.pysam.c:39:
/usr/include/inttypes.h:57:41: note: format string is defined here
57 | # define PRId64 __PRI64_PREFIX "d"
samtools/cram_size.c.pysam.c:564:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=]
564 | fprintf(outfp, "Format overhead size %18"PRId64"\n", end - tot_size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| off_t {aka long int}
/usr/include/inttypes.h:57:41: note: format string is defined here
57 | # define PRId64 __PRI64_PREFIX "d"
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-armv7l-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/reset.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcsamtools.o build/temp.linux-armv7l-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/cram_size.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/dict.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/lz4/lz4.o build/temp.linux-armv7l-cpython-311/samtools/padding.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/phase.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/reference.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/reset.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sample.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/samtools.pysam.o build/temp.linux-armv7l-cpython-311/samtools/stats.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/tmp_file.c.pysam.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armv7l-cpython-311/bcftools
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/hts.h:37,
from /usr/include/htslib/vcf.h:39,
from bcftools/vcfmerge.c.pysam.c:35:
/usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-armv7l-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/em.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/main.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/version.c.pysam.o build/temp.linux-armv7l-cpython-311/pysam/libcbcftools.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcutils.c -o build/temp.linux-armv7l-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/pysam_util.c -o build/temp.linux-armv7l-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcutils.o build/temp.linux-armv7l-cpython-311/pysam/pysam_util.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcsamtools.cpython-311-arm-linux-gnueabihf -lcbcftools.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:28625:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
28625 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:14308:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14308 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcalignmentfile.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-armv7l-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14382:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14382 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcalignedsegment.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-armv7l-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcfaidx.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcbcf.c -o build/temp.linux-armv7l-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
pysam/libcbcf.c:67290:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
67290 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
pysam/libcbcf.c:67015:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
67015 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
pysam/libcbcf.c:72149:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
72149 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
pysam/libcbcf.c:35361:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35361 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35387:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35387 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcbcf.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-armv7l-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcbgzf.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libctabixproxies.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/pysam -I/usr/include -I/<<PKGBUILDDIR>>/samtools -I/<<PKGBUILDDIR>>/samtools/lz4 -I/<<PKGBUILDDIR>>/bcftools -I/<<PKGBUILDDIR>> -I/usr/include/python3.11 -c pysam/libcvcf.c -o build/temp.linux-armv7l-cpython-311/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’:
pysam/libcvcf.c:25800:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized]
25800 | __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcvcf.c:20232:10: note: ‘__pyx_v_qual’ was declared here
20232 | double __pyx_v_qual;
| ^~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pysam/libcvcf.o -L/<<PKGBUILDDIR>>/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/tests/pysam_data'
samtools faidx ex1.fa
samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view --no-PG -bo ex2.bam ex2.sam
samtools index ex2.bam
samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view --no-PG -bo with_md.bam with_md.sam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view --no-PG -bu -o uncompressed.bam ex2.sam
samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam
samtools view --no-PG -bo MM-double.bam MM-double.sam
samtools view --no-PG -bo MM-multi.bam MM-multi.sam
samtools view --no-PG -bo MM-orient.bam MM-orient.sam
samtools view --no-PG -bo ex10.bam ex10.sam
samtools view --no-PG -bo ex3.bam ex3.sam
samtools view --no-PG -bo ex4.bam ex4.sam
samtools view --no-PG -bo ex5.bam ex5.sam
samtools view --no-PG -bo ex6.bam ex6.sam
samtools view --no-PG -bo ex8.bam ex8.sam
samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam
samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam
samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam
samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam
samtools view --no-PG -bo example_btag.bam example_btag.sam
samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam
samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam
samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam
samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam
touch tmp.list
samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam
rm -f tmp.list
samtools view --no-PG -bo issue100.bam issue100.sam
samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam
samtools view --no-PG -bo softclip.bam softclip.sam
samtools view --no-PG -bo tag_bug.bam tag_bug.sam
samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam
samtools view --no-PG -bo test_query_position.bam test_query_position.sam
samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam
samtools index MM-chebi.bam
samtools index MM-double.bam
samtools index MM-multi.bam
samtools index MM-orient.bam
samtools index ex10.bam
samtools index ex3.bam
samtools index ex4.bam
samtools index ex5.bam
samtools index ex6.bam
samtools index ex8.bam
samtools index ex9_fail.bam
samtools index ex9_nofail.bam
samtools index ex_spliced.bam
samtools index example_aligned_pairs.bam
samtools index example_btag.bam
samtools index example_dash_in_chr.bam
samtools index example_empty_header.bam
samtools index example_empty_with_header.bam
samtools index example_reverse_complement.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index issue100.bam
samtools index rg_with_tab.bam
samtools index softclip.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index test_query_position.bam
samtools index test_unaligned.bam
samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam
samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam
samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1
1+0 records in
1+0 records out
122292 bytes (122 kB, 119 KiB) copied, 0.00241224 s, 50.7 MB/s
(bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam
grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam -
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
touch all.stamp
rm with_md.sam
make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz # create tbi index
bcftools index example_vcf40.vcf.gz # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz # create tbi index
bcftools index example_vcf42.vcf.gz # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index
bcftools index example_vcf42_only_header.vcf.gz # create csi index
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz # create csi index
bgzip < example_vcf43.vcf > example_vcf43.vcf.gz
tabix -p vcf example_vcf43.vcf.gz # create tbi index
bcftools index example_vcf43.vcf.gz # create csi index
bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz
tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index
bcftools index example_vcf43_with_utf8.vcf.gz # create csi index
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf gnomad.vcf.gz # create tbi index
bcftools index gnomad.vcf.gz # create csi index
bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -p vcf gnomad_fixed.vcf.gz # create tbi index
bcftools index gnomad_fixed.vcf.gz # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz # create tbi index
bcftools index missing_genotypes.vcf.gz # create csi index
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf
bcftools index example_vcf43.bcf
bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf
bcftools index example_vcf43_with_utf8.bcf
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.bcf
bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools index gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
touch all.stamp
make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
dh_auto_test
I: pybuild base:291: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.11.5, pytest-7.4.2, pluggy-1.3.0 -- /usr/bin/python3.11
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>
configfile: setup.cfg
collecting ... collected 949 items
tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
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tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_34370eu_'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_34370eu_
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_g_linq__'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_g_linq__
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_fkhwnldp
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0hahvs54'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0hahvs54
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_5a54lmcg'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_5a54lmcg
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_hdligj97
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
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tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_bivqpxqrtmp_ex2.bam'
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_t3_69_w9tmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_h8qt2ayxtmp_multi.bam'
PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/0example_no_seq_in_header.bam'
PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam'
PASSED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex2_truncated.bam'
[E::bgzf_read_block] Failed to read BGZF block data at offset 105180 expected 17578 bytes; hread returned 17094
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex2_corrupt.bam'
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_88f9j7k0tmp_largecigar.bam'
PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo Fatal Python error: Bus error
Current thread 0xb6d8f020 (most recent call first):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/VariantFile_test.py", line 400 in <listcomp>
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/VariantFile_test.py", line 400 in testInfo
File "/usr/lib/python3.11/unittest/case.py", line 579 in _callTestMethod
File "/usr/lib/python3.11/unittest/case.py", line 623 in run
File "/usr/lib/python3.11/unittest/case.py", line 678 in __call__
File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 333 in runtest
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169 in pytest_runtest_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in __call__
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262 in <lambda>
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 261 in call_runtest_hook
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 222 in call_and_report
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 133 in runtestprotocol
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 350 in pytest_runtestloop
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 325 in _main
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 271 in wrap_session
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 318 in pytest_cmdline_main
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in __call__
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 169 in main
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 192 in console_main
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 in <module>
File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>", line 198 in _run_module_as_main
Extension modules: pysam.libcutils, pysam.libchtslib, pysam.libcsamtools, pysam.libcbcftools, pysam.libcfaidx, pysam.libctabixproxies, pysam.libctabix, pysam.libcalignmentfile, pysam.libcalignedsegment, pysam.libcsamfile, pysam.libcvcf, pysam.libcbcf, pysam.libcbgzf, Cython.Plex.Actions, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.Tempita._tempita, Cython.Compiler.Visitor, Cython.Compiler.FlowControl, _compile_test (total: 20)
Bus error
E: pybuild pybuild:395: test: plugin distutils failed with: exit code=135: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13
make[1]: *** [debian/rules:31: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2023-09-22T23:14:38Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 112920
Build-Time: 673
Distribution: trixie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 618
Job: python-pysam_0.21.0+ds-1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 1331
Source-Version: 0.21.0+ds-1
Space: 112920
Status: attempted
Version: 0.21.0+ds-1
--------------------------------------------------------------------------------
Finished at 2023-09-22T23:14:38Z
Build needed 00:22:11, 112920k disk space