python-pbh5tools →
0.8.0+dfsg-4 →
armhf → 2019-11-27 15:22:59
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| python-pbh5tools 0.8.0+dfsg-4 (armhf) Wed, 27 Nov 2019 15:02:11 +0000 |
+==============================================================================+
Package: python-pbh5tools
Version: 0.8.0+dfsg-4
Source Version: 0.8.0+dfsg-4
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-6094c5ff-f2c9-47f8-ac83-6fe9f9ad9f8d' 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 [12.9 MB]
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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-pbh5tools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/python-pbh5tools.git
Please use:
git clone git://anonscm.debian.org/debian-med/python-pbh5tools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8559 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main python-pbh5tools 0.8.0+dfsg-4 (dsc) [2287 B]
Get:2 http://172.17.0.1/private bullseye-staging/main python-pbh5tools 0.8.0+dfsg-4 (tar) [8550 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main python-pbh5tools 0.8.0+dfsg-4 (diff) [6140 B]
Fetched 8559 kB in 1s (9345 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pbh5tools-OhzV03/python-pbh5tools-0.8.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pbh5tools-OhzV03' 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-uBH5V0/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-uBH5V0/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-uBH5V0/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-uBH5V0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2615 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 31 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-uBH5V0/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 ... 12227 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 (>= 9), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-cram
Filtered Build-Depends: debhelper (>= 9), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-cram
dpkg-deb: building package 'sbuild-build-depends-python-pbh5tools-dummy' in '/<<BUILDDIR>>/resolver-uBH5V0/apt_archive/sbuild-build-depends-python-pbh5tools-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-pbh5tools-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-uBH5V0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Sources [530 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ Packages [612 B]
Fetched 2475 B in 1s (3231 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install python-pbh5tools 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 bsdmainutils ca-certificates cpp-9
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
dwz file g++-9 gcc-9 gcc-9-base gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libasan5 libatomic1 libblas3 libbrotli1
libbsd0 libcc1-0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-9-dev libgcc1
libgfortran5 libglib2.0-0 libgomp1 libgssapi-krb5-2 libhts2 libicu63
libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack3 libmagic-mgc libmagic1 libmpdec2
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib
libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1
libssl1.1 libstdc++-9-dev libstdc++6 libsub-override-perl libtinfo5 libtool
libubsan1 libuchardet0 libxml2 m4 man-db mime-support openssl po-debconf
python python-alabaster python-attr python-babel python-babel-localedata
python-certifi python-chardet python-cram python-docutils python-idna
python-imagesize python-jinja2 python-markupsafe python-minimal python-nose
python-numpy python-packaging python-pbcore python-pkg-resources
python-pygments python-pyparsing python-pysam python-requests python-roman
python-setuptools python-six python-sphinx python-typing python-tz
python-urllib3 python2 python2-minimal python2.7 python2.7-minimal python3
python3-distutils python3-lib2to3 python3-minimal python3.7
python3.7-minimal sensible-utils sgml-base sphinx-common xml-core
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-9-locales dh-make gcc-9-doc libstdc++6-9-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libquadmath0-dbg gettext-doc libasprintf-dev
libgettextpo-dev groff krb5-doc krb5-user libstdc++-9-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python-doc python-tk python-attr-doc fonts-linuxlibertine
| ttf-linux-libertine texlive-lang-french texlive-latex-base
texlive-latex-recommended python-jinja2-doc python-coverage python-nose-doc
gfortran python-dev python-pytest python-numpy-dbg python-numpy-doc
python-pbcore-doc python-pygments-doc ttf-bitstream-vera
python-pyparsing-doc python-cryptography python-openssl python-socks
python-setuptools-doc dvipng imagemagick-6.q16 latexmk libjs-mathjax
python-sphinx-rtd-theme python-stemmer sphinx-doc texlive-fonts-recommended
texlive-latex-extra texlive-plain-generic python-ntlm python2-doc
python2.7-doc binfmt-support python3-doc python3-tk python3-venv
python3.7-venv python3.7-doc sgml-base-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common krb5-locales publicsuffix libltdl-dev
libmail-sendmail-perl docutils-doc libpaper-utils python-pil python-h5py
python-enum34 python-cryptography python-ipaddress python-openssl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libblas3 libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl
libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5
libglib2.0-0 libgssapi-krb5-2 libhts2 libicu63 libjs-jquery libjs-sphinxdoc
libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblapack3 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1
libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
mime-support openssl po-debconf python python-alabaster python-attr
python-babel python-babel-localedata python-certifi python-chardet
python-cram python-docutils python-idna python-imagesize python-jinja2
python-markupsafe python-minimal python-nose python-numpy python-packaging
python-pbcore python-pkg-resources python-pygments python-pyparsing
python-pysam python-requests python-roman python-setuptools python-six
python-sphinx python-typing python-tz python-urllib3 python2 python2-minimal
python2.7 python2.7-minimal python3 python3-distutils python3-lib2to3
python3-minimal python3.7 python3.7-minimal
sbuild-build-depends-python-pbh5tools-dummy sensible-utils sgml-base
sphinx-common xml-core
The following packages will be upgraded:
cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libatomic1 libcc1-0 libgcc-9-dev
libgcc1 libgomp1 libstdc++-9-dev libstdc++6 libubsan1
13 upgraded, 113 newly installed, 0 to remove and 18 not upgraded.
Need to get 79.4 MB of archives.
After this operation, 201 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uBH5V0/apt_archive ./ sbuild-build-depends-python-pbh5tools-dummy 0.invalid.0 [892 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 libcc1-0 armhf 9.2.1-19+rpi1 [38.1 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.2.1-19+rpi1 [194 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libgcc1 armhf 1:9.2.1-19+rpi1 [36.9 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 9.2.1-19+rpi1 [73.7 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 9.2.1-19+rpi1 [8160 B]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.2.1-19+rpi1 [348 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 9.2.1-19+rpi1 [112 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf g++-9 armhf 9.2.1-19+rpi1 [7627 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-9-dev armhf 9.2.1-19+rpi1 [1707 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libgcc-9-dev armhf 9.2.1-19+rpi1 [640 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gcc-9 armhf 9.2.1-19+rpi1 [7284 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf cpp-9 armhf 9.2.1-19+rpi1 [6913 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 9.2.1-19+rpi1 [415 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.17-1 [395 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.17-1 [1107 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.17-2 [41.4 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.17-2 [21.1 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.17-1 [1823 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.17-1 [309 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.17-2 [20.9 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.17-2 [20.9 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.17-2 [41.7 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.17-2 [22.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.5-2 [584 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.5-2 [1527 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-1 [36.6 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.5-2 [1668 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.5-2 [347 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-1 [20.1 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-1 [61.5 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf sgml-base all 1.29.1 [15.0 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
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Get:62 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-2 [136 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.3-1 [1137 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf docutils-common all 0.15.2+dfsg-1 [167 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.8.0-8 [107 kB]
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Get:81 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
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Get:84 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.66.0-1+b1 [295 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.3-3 [76.4 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-19+rpi1 [230 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libjs-sphinxdoc all 1.8.5-3 [96.5 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.8.0-8 [1568 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf python-attr all 18.2.0-1 [37.2 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf python-pkg-resources all 41.2.0-1 [183 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf python-tz all 2019.3-1 [33.7 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf python-babel all 2.6.0+dfsg.1-1 [97.3 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf python-certifi all 2018.8.24-1 [140 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf python-chardet all 3.0.4-4 [80.6 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf python-cram all 0.7-3 [17.0 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf python-roman all 2.0.0-3 [8688 B]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf python-docutils all 0.15.2+dfsg-1 [383 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf python-idna all 2.6-2 [34.3 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf python-imagesize all 1.0.0-1 [4888 B]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python-markupsafe armhf 1.1.0-1 [13.7 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf python-jinja2 all 2.10.1-1 [106 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf python-nose all 1.3.7-4 [132 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf python-numpy armhf 1:1.16.5-1 [1918 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf python-pyparsing all 2.4.2-1 [106 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf python-six all 1.13.0-1 [16.2 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf python-packaging all 19.1-2 [23.8 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf python-pysam armhf 0.15.2+ds-2+rpi1 [1384 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf python-pbcore all 1.6.5+dfsg-1 [9100 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf python-pygments all 2.3.1+dfsg-1 [596 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf python-urllib3 all 1.24.1-1 [97.0 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf python-requests all 2.21.0-1 [67.1 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf python-setuptools all 41.2.0-1 [384 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf python-typing all 3.6.6-1 [22.7 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf sphinx-common all 1.8.5-3 [501 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf python-alabaster all 0.7.8-1 [18.4 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf python-sphinx all 1.8.5-3 [483 kB]
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Setting up libkrb5support0:armhf (1.17-6+b1) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
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Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
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Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
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update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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Setting up autoconf (2.69-11) ...
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Setting up python (2.7.17-2) ...
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Setting up gcc-9 (9.2.1-19+rpi1) ...
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Setting up gettext (0.19.8.1-10) ...
Setting up libstdc++-9-dev:armhf (9.2.1-19+rpi1) ...
Setting up python-typing (3.6.6-1) ...
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Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up python-pygments (2.3.1+dfsg-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
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Setting up g++-9 (9.2.1-19+rpi1) ...
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Setting up python-chardet (3.0.4-4) ...
Setting up python-requests (2.21.0-1) ...
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update-alternatives: using /usr/bin/pybabel-python2 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up python-packaging (19.1-2) ...
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Setting up dh-python (4.20191017) ...
Setting up libhts2:armhf (1.9-11) ...
Setting up python-numpy (1:1.16.5-1) ...
Setting up python-nose (1.3.7-4) ...
Setting up po-debconf (1.0.21) ...
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Setting up python-pysam (0.15.2+ds-2+rpi1) ...
Setting up python-pbcore (1.6.5+dfsg-1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.1) ...
Processing triggers for libc-bin (2.29-2+rpi1) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up docutils-common (0.15.2+dfsg-1) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up python-docutils (0.15.2+dfsg-1) ...
update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up python-sphinx (1.8.5-3) ...
update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode
update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode
update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode
update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode
Setting up sbuild-build-depends-python-pbh5tools-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-19+rpi1 gcc-9_9.2.1-19+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-19+rpi1 libstdc++6_9.2.1-19+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_3.5.46 bash_5.0-5 binutils_2.33.1-2+rpi1 binutils-arm-linux-gnueabihf_2.33.1-2+rpi1 binutils-common_2.33.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-19+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 docutils-common_0.15.2+dfsg-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-2 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+rpi1 g++-9_9.2.1-19+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-9_9.2.1-19+rpi1 gcc-9-base_9.2.1-19+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_1.22.4-3 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_9.2.1-19+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-19+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2+rpi1 libblas3_3.8.0-8 libblkid1_2.34-0.1 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-19+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.66.0-1+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdeflate0_1.3-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_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_9.2.1-19+rpi1 libgcc1_1:9.2.1-19+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-19+rpi1 libglib2.0-0_2.62.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-4 libgomp1_9.2.1-19+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 libjs-jquery_3.3.1~dfsg-3 libjs-sphinxdoc_1.8.5-3 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 liblapack3_3.8.0-8 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-1 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 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_10.32-5 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.17-2 libpython2-stdlib_2.7.17-2 libpython2.7-minimal_2.7.17-1 libpython2.7-stdlib_2.7.17-1 libpython3-stdlib_3.7.5-1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-19+rpi1 libstdc++6_9.2.1-19+rpi1 libsub-override-perl_0.09-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-19+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 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_5.6 openssl_1.1.1d-2 passwd_1:4.7-2 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-alabaster_0.7.8-1 python-attr_18.2.0-1 python-babel_2.6.0+dfsg.1-1 python-babel-localedata_2.6.0+dfsg.1-1 python-certifi_2018.8.24-1 python-chardet_3.0.4-4 python-cram_0.7-3 python-docutils_0.15.2+dfsg-1 python-idna_2.6-2 python-imagesize_1.0.0-1 python-jinja2_2.10.1-1 python-markupsafe_1.1.0-1 python-minimal_2.7.17-2 python-nose_1.3.7-4 python-numpy_1:1.16.5-1 python-packaging_19.1-2 python-pbcore_1.6.5+dfsg-1 python-pkg-resources_41.2.0-1 python-pygments_2.3.1+dfsg-1 python-pyparsing_2.4.2-1 python-pysam_0.15.2+ds-2+rpi1 python-requests_2.21.0-1 python-roman_2.0.0-3 python-setuptools_41.2.0-1 python-six_1.13.0-1 python-sphinx_1.8.5-3 python-typing_3.6.6-1 python-tz_2019.3-1 python-urllib3_1.24.1-1 python2_2.7.17-2 python2-minimal_2.7.17-2 python2.7_2.7.17-1 python2.7-minimal_2.7.17-1 python3_3.7.5-1 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-1 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pbh5tools-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sgml-base_1.29.1 sphinx-common_1.8.5-3 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xml-core_0.18+nmu1 xz-utils_5.2.4-1 zlib1g_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 Feb 15 07:44:13 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pbh5tools_0.8.0+dfsg-4.dsc
dpkg-source: info: extracting python-pbh5tools in /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg
dpkg-source: info: unpacking python-pbh5tools_0.8.0+dfsg.orig.tar.gz
dpkg-source: info: unpacking python-pbh5tools_0.8.0+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying default-doc-theme
dpkg-source: info: applying pbcore-change.patch
dpkg-source: info: applying verbose-testing.patch
dpkg-source: info: applying override-test-failure.patch
dpkg-source: info: applying ignore-cram-results.patch
dpkg-source: info: applying fix-type-in-test.patch
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-6094c5ff-f2c9-47f8-ac83-6fe9f9ad9f8d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package python-pbh5tools
dpkg-buildpackage: info: source version 0.8.0+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
LC_ALL=C.UTF-8 dh clean --with python2 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_auto_clean
I: pybuild base:217: python2.7 setup.py clean
running clean
removing '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/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
/usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
cd doc && rm -rf modules.rst pbtools.* bash5lib.* cmph5tools.* \
bash5tools.* _templates _static _build searchindex.js objects.inv
rm -rf build/;\
find . -name "*.egg-info" | xargs rm -rf;\
find . -name "*.pyc" | xargs rm -rf;\
rm -rf dist/
rm -f nosetests.xml
make[2]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
LC_ALL=C.UTF-8 dh build-arch --with python2 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:217: python2.7 setup.py config
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_auto_build
I: pybuild base:217: /usr/bin/python setup.py build
running build
running build_py
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Compare.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Format.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Merge.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Select.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Sort.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Stats.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/CmpH5Utils.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/Indexer.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/Metrics.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/PBH5ToolsException.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/__init__.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/_version.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/cbook.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
copying ./pbh5tools/mlab.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools
running build_ext
building 'pbh5tools/ci' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/pbh5tools
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pbh5tools/ci.c -o build/temp.linux-armhf-2.7/pbh5tools/ci.o -O3 -shared
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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pbh5tools/ci.o -o /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.so
running build_scripts
creating build/scripts-2.7
copying and adjusting bin/bash5tools.py -> build/scripts-2.7
copying and adjusting bin/cmph5tools.py -> build/scripts-2.7
changing mode of build/scripts-2.7/bash5tools.py from 664 to 775
changing mode of build/scripts-2.7/cmph5tools.py from 664 to 775
/usr/bin/make -C doc html
make[2]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/doc'
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v1.8.5
making output directory...
loading intersphinx inventory from http://docs.python.org/objects.inv...
intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 2 source files that are out of date
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] cmph5tools-examples
reading sources... [100%] index
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 50%] cmph5tools-examples
writing output... [100%] index
generating indices... genindex
writing additional pages... search
copying static files... WARNING: html_static_path entry u'/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/doc/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 1 warning.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
make[2]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/doc'
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="PATH=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7:$PATH /usr/bin/make test" \
dh_auto_test
I: pybuild base:217: PATH=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/make test
make[2]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
cram -v doc/examples.t
doc/examples.t: failed
--- doc/examples.t
+++ doc/examples.t.err
@@ -14,95 +14,64 @@
take 50% of the reads
$ cmph5tools.py select --where "SubSample(.5)" $INCMP --outFile ss.cmp.h5
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ test -f ss.cmp.h5
+ [1]
## Example 2: produce tabular data from a cmp.h5 file
$ cmph5tools.py stats --what "Tbl(q = Percentile(ReadLength, 90), m = Median(Accuracy))" \
> --groupBy Barcode $INCMP | tail
- F_44--R_44 516.80 0.90
- F_45--R_45 534.60 0.90
- F_46--R_46 517.80 0.90
- F_47--R_47 515.80 0.91
- F_48--R_48 624.20 0.91
- F_5--R_5 571.60 0.90
- F_6--R_6 507.90 0.90
- F_7--R_7 572.40 0.90
- F_8--R_8 574.40 0.91
- F_9--R_9 485.60 0.90
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
## Example 3: query the package to determine the available metrics and statistics
$ cmph5tools.py listMetrics
- --- Metrics:
- ByFactor[metric, factor, statistic]\t (esc)
- _MoleculeReadStart\t (esc)
- _MinSubreadLength\t (esc)
- _MaxSubreadLength\t (esc)
- _UnrolledReadLength\t (esc)
- DefaultWhere\t (esc)
- DefaultGroupBy\t (esc)
- TemplateSpan
- \tThe number of template bases covered by the read\t (esc)
- ReadLength\t (esc)
- NErrors\t (esc)
- ReadDuration\t (esc)
- FrameRate\t (esc)
- IPD\t (esc)
- PulseWidth\t (esc)
- Movie\t (esc)
- Reference\t (esc)
- RefIdentifier\t (esc)
- HoleNumber\t (esc)
- ReadStart\t (esc)
- ReadEnd\t (esc)
- TemplateStart\t (esc)
- TemplateEnd\t (esc)
- MoleculeId\t (esc)
- MoleculeName\t (esc)
- Strand\t (esc)
- AlignmentIdx\t (esc)
- Barcode\t (esc)
- AverageBarcodeScore\t (esc)
- MapQV\t (esc)
- WhiteList\t (esc)
- SubSample[rate, n]
- \tboolean vector with true occuring at rate rate or nreads = n (esc)
-
- --- Statistics:
- Min\t (esc)
- Max\t (esc)
- Sum\t (esc)
- Mean\t (esc)
- Median\t (esc)
- Count\t (esc)
- Percentile[metric, ptile]\t (esc)
- Round[metric, digits]
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
## Example 4: Familiar SQL-like syntax
$ cmph5tools.py stats --what "Tbl(a=Accuracy,b=Barcode)" \
> --where "Barcode == 'F_28--R_28'" \
> --groupBy Reference $INCMP
- Group a b
- EGFR_600_t29_1 0.91 F_28--R_28
- EGFR_600_t29_1 0.91 F_28--R_28
- EGFR_600_t29_1 0.95 F_28--R_28
- EGFR_600_t29_1 0.93 F_28--R_28
- EGFR_600_t29_1 0.91 F_28--R_28
- EGFR_600_t29_1 0.90 F_28--R_28
- EGFR_600_t29_1 0.94 F_28--R_28
- EGFR_600_t29_1 0.93 F_28--R_28
- EGFR_600_t9_1 0.86 F_28--R_28
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
## Example 5: Familiar SQL-like functions
$ cmph5tools.py stats --what "Count(Reference)" \
> --where "Barcode == 'F_10--R_10'" \
> --groupBy Reference $INCMP
- Group Count(Reference)
- EGFR_600_t11_1 62
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
## Handling IPD, PulseWidth, and Base-level Metrics
@@ -113,13 +82,13 @@
$ cmph5tools.py stats --where "(Barcode == 'F_10--R_10') & (Accuracy > .95)" \
> --what "Tbl(idx = AlignmentIdx, ipd = Median(IPD), pw = Median(PulseWidth))" \
> $INCMP
- ipd pw idx
- 15.50 11.50 562
- 9.00 10.00 563
- 11.00 10.00 589
- 13.00 11.00 603
- 14.00 10.50 626
- 8.00 13.00 627
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
**NOTE:** The '(' surrounding the clauses in the where predicate are
@@ -132,75 +101,48 @@
selection to produce plots on very arbitrary splits.
$ cmph5tools.py select --where "Accuracy > .95" $INCMP
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py summarize out.cmp.h5
- ----------------------------------------
- filename: out.cmp.h5
- version: 1.3.1.PB
- n reads: 91
- n refs: 49
- n movies: 4
- n bases: 15315
- avg rl: 168
- avg acc: 0.9658
-
- \t Movie Summary: (esc)
- Group nBases avgAccuracy avgReadLength
- m121005_190843_42142_c100376662550000001523029810101285_s1_p0 4770 1.0 170.4
- m121005_190843_42142_c100376662550000001523029810101285_s2_p0 2259 1.0 173.8
- m121005_210848_42142_c100376662550000001523029810101286_s1_p0 6167 1.0 192.7
- m121005_210848_42142_c100376662550000001523029810101286_s2_p0 2119 1.0 117.7
-
- \t Reference Summary: (esc)
- Group nBases avgAccuracy avgReadLength
- EGFR_600_t11_1 1396 1.0 232.7
- EGFR_600_t13_1 83 1.0 41.5
- EGFR_600_t15_1 252 1.0 126.0
- EGFR_600_t16_1 50 1.0 25.0
- EGFR_600_t17_1 531 1.0 531.0
- EGFR_600_t19_1 705 1.0 235.0
- EGFR_600_t20_1 184 1.0 184.0
- EGFR_600_t21_1 122 1.0 122.0
- EGFR_600_t23_1 553 1.0 276.5
- EGFR_600_t24_1 32 1.0 32.0
- EGFR_600_t25_1 531 1.0 265.5
- EGFR_600_t26_1 55 1.0 27.5
- EGFR_600_t27_1 148 1.0 148.0
- EGFR_600_t28_1 91 1.0 30.3
- EGFR_600_t2_1 239 1.0 59.8
- EGFR_600_t3_1 462 1.0 462.0
- EGFR_600_t4_1 701 1.0 350.5
- EGFR_600_t5_1 147 1.0 49.0
- EGFR_600_t6_1 201 1.0 50.2
- EGFR_600_t7_1 873 1.0 436.5
- EGFR_600_t9_1 562 1.0 112.4
- MET_600_t2_1 42 1.0 42.0
- MET_600_t2_11 681 1.0 227.0
- MET_600_t2_13 448 1.0 448.0
- MET_600_t2_14 223 1.0 223.0
- MET_600_t2_15 43 1.0 43.0
- MET_600_t2_16 671 1.0 167.8
- MET_600_t2_17 44 1.0 44.0
- MET_600_t2_18 701 1.0 175.2
- MET_600_t2_19 546 1.0 182.0
- MET_600_t2_2 186 1.0 93.0
- MET_600_t2_20 394 1.0 98.5
- MET_600_t2_21 71 1.0 35.5
- MET_600_t2_3 655 1.0 218.3
- MET_600_t2_4 1321 1.0 330.2
- MET_600_t2_5 500 1.0 500.0
- MET_600_t2_6 120 1.0 120.0
- MET_600_t2_7 660 1.0 220.0
- MET_600_t2_8 24 1.0 24.0
- MET_600_t2_9 67 1.0 67.0
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
## Selection
$ cmph5tools.py select --groupBy Barcode \
> --where "(Barcode == 'F_42--R_42') | (Barcode == 'F_10--R_10')" $INCMP
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py merge --outFile merged.cmp.h5 F_42--R_42.cmp.h5 F_10--R_10.cmp.h5
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py stats --what "Count(Reference)" --groupBy Barcode merged.cmp.h5
- Group Count(Reference)
- F_10--R_10 62
- F_42--R_42 76
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
cmp.h5 files can also be split by a pre-defined csv file with three columns.
@@ -208,50 +150,46 @@
names are metrics from 'cmph5tools.py listMetrics'
$ export INCSV=$TESTDIR/../etc/grouped.csv
$ cmph5tools.py select --groupByCsv $INCSV $INCMP
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py stats grpA.cmp.h5
- readLength accuracy
- 426 0.90
- 538 0.92
- 552 0.92
- 589 0.89
- 538 0.92
- 129 0.91
- 118 0.83
- 126 0.85
- 239 0.92
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py stats grpB.cmp.h5
- readLength accuracy
- 156 0.92
- 347 0.86
- 531 0.92
- 550 0.93
- 122 0.80
- 86 0.93
- 132 0.90
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py stats grpC.cmp.h5
- readLength accuracy
- 151 0.90
- 193 0.90
- 439 0.90
- 546 0.90
- 563 0.90
- 565 0.92
- 568 0.89
- 148 0.95
- 59 0.88
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
$ cmph5tools.py stats grpD.cmp.h5
- readLength accuracy
- 95 0.94
- 304 0.88
- 455 0.95
- 489 0.86
- 584 0.87
- 558 0.90
- 567 0.87
- 543 0.90
- 170 0.98
- 171 0.82
+ Traceback (most recent call last):
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7/cmph5tools.py", line 43, in <module>
+ from pbh5tools.CmpH5Select import cmpH5Select
+ File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py", line 38, in <module>
+ import h5py as H5
+ ImportError: No module named h5py
+ [1]
**NOTE:** One of the reasons that the cmp.h5 file format is appealing
is that you don't need to split it to access particular strata. In
# Ran 1 tests, 0 skipped, 1 failed.
make[2]: [Makefile:26: examples] Error 1 (ignored)
sed 's/^ / /' doc/examples.t > doc/examples.md
find tests -name "*.py" | xargs nosetests -v
Failure: ImportError (No module named h5py) ... ERROR
Failure: ImportError (No module named h5py) ... ERROR
======================================================================
ERROR: Failure: ImportError (No module named h5py)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/tests/test_cmph5lib_CmpH5Merge.py", line 9, in <module>
from pbh5tools.CmpH5Select import cmpH5Select
File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/pbh5tools/CmpH5Select.py", line 38, in <module>
import h5py as H5
ImportError: No module named h5py
======================================================================
ERROR: Failure: ImportError (No module named h5py)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/tests/test_cmph5lib_CmpH5Sort.py", line 5, in <module>
import h5py as h
ImportError: No module named h5py
----------------------------------------------------------------------
Ran 2 tests in 0.008s
FAILED (errors=2)
make[2]: *** [Makefile:20: test] Error 123
make[2]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
E: pybuild pybuild:341: test: plugin custom failed with: exit code=2: PATH=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/make test
dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 returned exit code 13
make[1]: *** [debian/rules:26: override_dh_auto_test] Error 255
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
make: *** [debian/rules:11: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-11-27T15:22:55Z
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: 74
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1119
Job: python-pbh5tools_0.8.0+dfsg-4
Machine Architecture: armhf
Package: python-pbh5tools
Package-Time: 1244
Source-Version: 0.8.0+dfsg-4
Space: 0
Status: failed
Version: 0.8.0+dfsg-4
--------------------------------------------------------------------------------
Finished at 2019-11-27T15:22:55Z
Build needed 00:00:00, 0k disc space