python-pysam →
0.15.3+ds-5 →
armhf → 2020-01-10 00:17:02
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| python-pysam 0.15.3+ds-5 (armhf) Thu, 09 Jan 2020 23:54:24 +0000 |
+==============================================================================+
Package: python-pysam
Version: 0.15.3+ds-5
Source Version: 0.15.3+ds-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-cb86d24c-0a77-4fcc-b150-bd9f864d73ce' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 31s (794 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 1740 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.3+ds-5 (dsc) [2561 B]
Get:2 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.3+ds-5 (tar) [1364 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.3+ds-5 (diff) [373 kB]
Fetched 1740 kB in 1s (1893 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-manX6l/python-pysam-0.15.3+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-manX6l' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-osd7aM/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-osd7aM/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-osd7aM/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2854 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12242 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
Filtered Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-osd7aM/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-pysam-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Sources [600 B]
Get:5 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ Packages [666 B]
Fetched 2599 B in 1s (3269 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install python-pysam build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu63 libjs-jquery
libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev
libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db mime-support po-debconf python python-all python-all-dev
python-atomicwrites python-attr python-configparser python-contextlib2
python-dev python-funcsigs python-importlib-metadata python-minimal
python-more-itertools python-packaging python-pathlib2 python-pkg-resources
python-pluggy python-py python-pyparsing python-pytest python-scandir
python-setuptools python-six python-wcwidth python-zipp python2 python2-dev
python2-minimal python2.7 python2.7-dev python2.7-minimal python3
python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev
python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal
python3-more-itertools python3-packaging python3-pkg-resources
python3-pluggy python3-py python3-pyparsing python3-pytest
python3-setuptools python3-six python3-wcwidth python3-zipp python3.7
python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal
samtools sensible-utils tabix zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib
texlive-latex-recommended wamerican | wordlist whois vacation cython-doc
dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk
python-attr-doc python-funcsigs-doc subversion python-pytest-xdist
python-pyparsing-doc python-mock python-setuptools-doc python2-doc
python2.7-doc binfmt-support python3-doc python3-tk python3-venv
python3.7-venv python3.7-doc python3.8-venv python3.8-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs javascript-common krb5-locales libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu63 libjs-jquery
libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev
libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db mime-support po-debconf python python-all python-all-dev
python-atomicwrites python-attr python-configparser python-contextlib2
python-dev python-funcsigs python-importlib-metadata python-minimal
python-more-itertools python-packaging python-pathlib2 python-pkg-resources
python-pluggy python-py python-pyparsing python-pytest python-scandir
python-setuptools python-six python-wcwidth python-zipp python2 python2-dev
python2-minimal python2.7 python2.7-dev python2.7-minimal python3
python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev
python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal
python3-more-itertools python3-packaging python3-pkg-resources
python3-pluggy python3-py python3-pyparsing python3-pytest
python3-setuptools python3-six python3-wcwidth python3-zipp python3.7
python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal
samtools sbuild-build-depends-python-pysam-dummy sensible-utils tabix
zlib1g-dev
0 upgraded, 145 newly installed, 0 to remove and 0 not upgraded.
Need to get 164 MB of archives.
After this operation, 357 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-osd7aM/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [956 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-1 [29.5 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.17-1 [395 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.17-1 [1107 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.17-2 [41.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.17-2 [21.1 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.17-1 [1823 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.17-1 [309 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.17-2 [20.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.17-2 [20.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.17-2 [41.7 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.17-2 [22.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1 [585 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1 [1527 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1 [1669 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1 [350 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.1-2 [742 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.1-2 [1620 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-1 [78.0 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-12 [275 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf bcftools armhf 1.9-1 [449 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf cython armhf 0.29.14-0.1 [1355 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf cython3 armhf 0.29.14-0.1 [1375 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.3 [174 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2 [25.3 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.9-1 [119 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-12 [4141 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libjs-sphinxdoc all 1.8.5-4 [96.7 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7 armhf 2.7.17-1 [883 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-dev armhf 2.7.17-1 [26.5 MB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libpython2-dev armhf 2.7.17-2 [21.0 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libpython-dev armhf 2.7.17-2 [21.0 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libpython-all-dev armhf 2.7.17-2 [1068 B]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7 armhf 3.7.6-1 [1253 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-dev armhf 3.7.6-1 [40.2 MB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.7.5-3 [20.3 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.1-2 [1597 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8 armhf 3.8.1-2 [1361 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-dev armhf 3.8.1-2 [46.0 MB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libpython3-all-dev armhf 3.7.5-3 [1072 B]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf python-all armhf 2.7.17-2 [1048 B]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf python2.7-dev armhf 2.7.17-1 [284 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf python2-dev armhf 2.7.17-2 [1224 B]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf python-dev armhf 2.7.17-2 [1196 B]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf python-all-dev armhf 2.7.17-2 [1072 B]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf python-atomicwrites all 1.1.5-2 [6808 B]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf python-attr all 18.2.0-1 [37.2 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf python-configparser all 3.5.0b2-3 [62.6 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf python-contextlib2 all 0.5.5-3 [12.6 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf python-funcsigs all 1.0.2-4 [13.7 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python-six all 1.13.0-1 [16.2 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf python-scandir armhf 1.10.0-2 [17.2 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf python-pathlib2 all 2.3.5-1 [19.6 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf python-more-itertools all 4.2.0-1 [42.3 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf python-zipp all 0.6.0-1 [5768 B]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf python-importlib-metadata all 0.23-2 [9296 B]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf python-pyparsing all 2.4.2-1 [106 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf python-packaging all 19.1-2 [23.8 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf python-pkg-resources all 41.2.0-1 [183 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf python-pluggy all 0.13.0-2 [21.8 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf python-py all 1.8.0-1 [86.5 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf python-wcwidth all 0.1.7+dfsg1-6 [15.4 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf python-pytest all 4.6.7-1 [266 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf python-setuptools all 41.2.0-1 [384 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.1-2 [406 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf python3-all armhf 3.7.5-3 [1060 B]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf python3.7-dev armhf 3.7.6-1 [518 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.7.5-3 [1260 B]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf python3.8-dev armhf 3.8.1-2 [519 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf python3-all-dev armhf 3.7.5-3 [1076 B]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf python3-atomicwrites all 1.1.5-2 [6892 B]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf python3-attr all 18.2.0-1 [37.3 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.13.0-1 [16.2 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf python3-more-itertools all 4.2.0-1 [42.2 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf python3-zipp all 0.6.0-1 [5856 B]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf python3-importlib-metadata all 0.23-2 [9356 B]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.2-1 [106 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 19.1-2 [23.9 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.2.0-1 [154 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf python3-pluggy all 0.13.0-2 [21.9 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf python3-py all 1.8.0-1 [86.5 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf python3-wcwidth all 0.1.7+dfsg1-6 [15.5 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf python3-pytest all 4.6.7-1 [266 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 41.2.0-1 [307 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.9-7 [399 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf tabix armhf 1.9-12 [249 kB]
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Processing triggers for libc-bin (2.29-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 bcftools_1.9-1 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-22+rpi1 cython_0.29.14-0.1 cython3_0.29.14-0.1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-22+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdeflate0_1.5-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-12 libhts2_1.9-12 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjs-jquery_3.3.1~dfsg-3 libjs-sphinxdoc_1.8.5-4 libjs-underscore_1.9.1~dfsg-1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-1 libpsl5_0.20.2-2 libpython-all-dev_2.7.17-2 libpython-dev_2.7.17-2 libpython-stdlib_2.7.17-2 libpython2-dev_2.7.17-2 libpython2-stdlib_2.7.17-2 libpython2.7_2.7.17-1 libpython2.7-dev_2.7.17-1 libpython2.7-minimal_2.7.17-1 libpython2.7-stdlib_2.7.17-1 libpython3-all-dev_3.7.5-3 libpython3-dev_3.7.5-3 libpython3-stdlib_3.7.5-3 libpython3.7_3.7.6-1 libpython3.7-dev_3.7.6-1 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libpython3.8_3.8.1-2 libpython3.8-dev_3.8.1-2 libpython3.8-minimal_3.8.1-2 libpython3.8-stdlib_3.8.1-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python_2.7.17-2 python-all_2.7.17-2 python-all-dev_2.7.17-2 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-configparser_3.5.0b2-3 python-contextlib2_0.5.5-3 python-dev_2.7.17-2 python-funcsigs_1.0.2-4 python-importlib-metadata_0.23-2 python-minimal_2.7.17-2 python-more-itertools_4.2.0-1 python-packaging_19.1-2 python-pathlib2_2.3.5-1 python-pkg-resources_41.2.0-1 python-pluggy_0.13.0-2 python-py_1.8.0-1 python-pyparsing_2.4.2-1 python-pytest_4.6.7-1 python-scandir_1.10.0-2 python-setuptools_41.2.0-1 python-six_1.13.0-1 python-wcwidth_0.1.7+dfsg1-6 python-zipp_0.6.0-1 python2_2.7.17-2 python2-dev_2.7.17-2 python2-minimal_2.7.17-2 python2.7_2.7.17-1 python2.7-dev_2.7.17-1 python2.7-minimal_2.7.17-1 python3_3.7.5-3 python3-all_3.7.5-3 python3-all-dev_3.7.5-3 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.5-3 python3-distutils_3.8.0-1 python3-importlib-metadata_0.23-2 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-3 python3-more-itertools_4.2.0-1 python3-packaging_19.1-2 python3-pkg-resources_41.2.0-1 python3-pluggy_0.13.0-2 python3-py_1.8.0-1 python3-pyparsing_2.4.2-1 python3-pytest_4.6.7-1 python3-setuptools_41.2.0-1 python3-six_1.13.0-1 python3-wcwidth_0.1.7+dfsg1-6 python3-zipp_0.6.0-1 python3.7_3.7.6-1 python3.7-dev_3.7.6-1 python3.7-minimal_3.7.6-1 python3.8_3.8.1-2 python3.8-dev_3.8.1-2 python3.8-minimal_3.8.1-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 samtools_1.9-7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tabix_1.9-12 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jan 6 17:28:20 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.3+ds-5.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.15.3+ds
dpkg-source: info: unpacking python-pysam_0.15.3+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.15.3+ds-5.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 spelling
dpkg-source: info: applying hts1.10
dpkg-source: info: applying samtools_v1.10_full
dpkg-source: info: applying bcftools_v1.10_full
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-cb86d24c-0a77-4fcc-b150-bd9f864d73ce
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.15.3+ds-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/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 python2,python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
dh_auto_clean
I: pybuild base:217: python2.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:217: python3.8 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.8' does not exist -- can't clean it
I: pybuild base:217: python3.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.7' 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 '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python2,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:217: python2.7 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.8 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.7 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:217: /usr/bin/python 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 /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libchtslib.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcsamtools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcbcftools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcutils.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcalignmentfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2530:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2535:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2540:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcsamfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcalignedsegment.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libctabix.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcfaidx.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcbcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcbgzf.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libctabixproxies.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcvcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/pysam
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
creating build/temp.linux-armhf-2.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-armhf-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from samtools/bam_color.c.pysam.c:30:
samtools/bam.h: In function ‘bam_header_init’:
samtools/bam.h:245:64: warning: implicit declaration of function ‘sam_hdr_init’; did you mean ‘bam_hdr_init’? [-Wimplicit-function-declaration]
245 | static inline bam_header_t *bam_header_init(void) { return sam_hdr_init(); }
| ^~~~~~~~~~~~
| bam_hdr_init
samtools/bam.h:245:64: warning: returning ‘int’ from a function with return type ‘bam_header_t *’ {aka ‘struct <anonymous> *’} makes pointer from integer without a cast [-Wint-conversion]
245 | static inline bam_header_t *bam_header_init(void) { return sam_hdr_init(); }
| ^~~~~~~~~~~~~~
samtools/bam.h: In function ‘bam_header_destroy’:
samtools/bam.h:251:67: warning: implicit declaration of function ‘sam_hdr_destroy’; did you mean ‘bam_hdr_destroy’? [-Wimplicit-function-declaration]
251 | static inline void bam_header_destroy(bam_header_t *header) { sam_hdr_destroy(header); }
| ^~~~~~~~~~~~~~~
| bam_hdr_destroy
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from samtools/bam.c.pysam.c:33:
samtools/bam.h: In function ‘bam_header_init’:
samtools/bam.h:245:64: warning: implicit declaration of function ‘sam_hdr_init’; did you mean ‘bam_hdr_init’? [-Wimplicit-function-declaration]
245 | static inline bam_header_t *bam_header_init(void) { return sam_hdr_init(); }
| ^~~~~~~~~~~~
| bam_hdr_init
samtools/bam.h:245:64: warning: returning ‘int’ from a function with return type ‘bam_header_t *’ {aka ‘struct <anonymous> *’} makes pointer from integer without a cast [-Wint-conversion]
245 | static inline bam_header_t *bam_header_init(void) { return sam_hdr_init(); }
| ^~~~~~~~~~~~~~
samtools/bam.h: In function ‘bam_header_destroy’:
samtools/bam.h:251:67: warning: implicit declaration of function ‘sam_hdr_destroy’; did you mean ‘bam_hdr_destroy’? [-Wimplicit-function-declaration]
251 | static inline void bam_header_destroy(bam_header_t *header) { sam_hdr_destroy(header); }
| ^~~~~~~~~~~~~~~
| bam_hdr_destroy
samtools/bam.c.pysam.c: In function ‘bam_validate1’:
samtools/bam.c.pysam.c:63:35: warning: implicit declaration of function ‘sam_hdr_nref’; did you mean ‘sam_hdr_read’? [-Wimplicit-function-declaration]
63 | if (header && (b->core.tid >= sam_hdr_nref(header) || b->core.mtid >= sam_hdr_nref(header))) return 0;
| ^~~~~~~~~~~~
| sam_hdr_read
samtools/bam.c.pysam.c: In function ‘bam_get_library’:
samtools/bam.c.pysam.c:90:9: warning: implicit declaration of function ‘sam_hdr_find_tag_id’ [-Wimplicit-function-declaration]
90 | if (sam_hdr_find_tag_id(h, "RG", "ID", rg, "LB", &lib) < 0)
| ^~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from samtools/bam2bcf.c.pysam.c:38:
samtools/bam2bcf.h:103:5: error: unknown type name ‘hts_pos_t’
103 | hts_pos_t pos;
| ^~~~~~~~~
samtools/bam2bcf.h:132:67: error: unknown type name ‘hts_pos_t’; did you mean ‘hts_itr_t’?
132 | int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, hts_pos_t pos, bcf_callaux_t *bca, const char *ref,
| ^~~~~~~~~
| hts_itr_t
error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
E: pybuild pybuild:341: build: plugin distutils failed with: exit code=1: /usr/bin/python setup.py build
dh_auto_build: pybuild --build --test-pytest -i python{version} -p 2.7 returned exit code 13
make: *** [debian/rules:24: build-arch] Error 255
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-01-10T00:16:55Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 276
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1009
Job: python-pysam_0.15.3+ds-5
Machine Architecture: armhf
Package: python-pysam
Package-Time: 1351
Source-Version: 0.15.3+ds-5
Space: 0
Status: failed
Version: 0.15.3+ds-5
--------------------------------------------------------------------------------
Finished at 2020-01-10T00:16:55Z
Build needed 00:00:00, 0k disc space