python-biom-format →
2.1.8+dfsg-3+b1 →
armhf → 2020-09-01 16:58:17
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| python-biom-format 2.1.8+dfsg-3+b1 (armhf) Tue, 01 Sep 2020 16:39:32 +0000 |
+==============================================================================+
Package: python-biom-format
Version: 2.1.8+dfsg-3+b1
Source Version: 2.1.8+dfsg-3
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-d4a24d84-278f-43ac-93bc-8ea0925c092e' with '<<CHROOT>>'
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| Update chroot |
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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 [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
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| Fetch source files |
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Check APT
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Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-biom-format' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-biom-format.git
Please use:
git clone https://salsa.debian.org/med-team/python-biom-format.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8541 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main python-biom-format 2.1.8+dfsg-3 (dsc) [2570 B]
Get:2 http://172.17.0.1/private bullseye-staging/main python-biom-format 2.1.8+dfsg-3 (tar) [8528 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main python-biom-format 2.1.8+dfsg-3 (diff) [10.4 kB]
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I: NOTICE: Log filtering will replace 'build/python-biom-format-C11kQ8/python-biom-format-2.1.8+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-biom-format-C11kQ8' with '<<BUILDDIR>>'
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| Install build-essential |
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Setup apt archive
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-A7nj2C/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-A7nj2C/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-A7nj2C/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-A7nj2C/apt_archive ./ InRelease
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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:
bsdextrautils netbase sensible-utils
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 46 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-A7nj2C/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12517 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-amd64 any-arm64 any-i386 any-mips64el any-ppc64el armel armhf mipsel all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, help2man, bash-completion, cython3, python3-all-dev, python3-click, python3-future, python3-h5py, python3-nose, python3-numpy, python3-pandas, python3-setuptools, python3-scipy, python3-sphinx, python3-matplotlib
Filtered Build-Depends: debhelper-compat (= 13), dh-python, help2man, bash-completion, cython3, python3-all-dev, python3-click, python3-future, python3-h5py, python3-nose, python3-numpy, python3-pandas, python3-setuptools, python3-scipy, python3-sphinx, python3-matplotlib
dpkg-deb: building package 'sbuild-build-depends-python-biom-format-dummy' in '/<<BUILDDIR>>/resolver-A7nj2C/apt_archive/sbuild-build-depends-python-biom-format-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-biom-format-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-A7nj2C/apt_archive ./ InRelease
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Get:4 copy:/<<BUILDDIR>>/resolver-A7nj2C/apt_archive ./ Sources [588 B]
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Reading package lists...
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Reading package lists...
Install python-biom-format build dependencies (apt-based resolver)
------------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bash-completion ca-certificates
cpp-10 cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism
docutils-common dwz file fonts-lyx g++-10 gcc-10 gcc-10-base gettext
gettext-base groff-base help2man intltool-debian libaec0 libarchive-zip-perl
libasan6 libatomic1 libblas3 libbrotli1 libcc1-0 libcroco3 libdebhelper-perl
libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
libfreetype6 libgcc-10-dev libgcc-s1 libgfortran5 libglib2.0-0 libgomp1
libhdf5-103-1 libhdf5-hl-100 libicu67 libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libmagic-mgc
libmagic1 libpipeline1 libpng16-16 libpython3-all-dev libpython3-dev
libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libssl1.1 libstdc++-10-dev libstdc++6
libsub-override-perl libsz2 libtool libubsan1 libuchardet0 libxml2 m4 man-db
mime-support node-jquery openssl po-debconf python-babel-localedata
python-matplotlib-data python3 python3-alabaster python3-all python3-all-dev
python3-babel python3-certifi python3-chardet python3-click python3-colorama
python3-cycler python3-dateutil python3-decorator python3-dev
python3-distutils python3-docutils python3-future python3-h5py
python3-h5py-serial python3-idna python3-imagesize python3-jinja2
python3-kiwisolver python3-lib2to3 python3-markupsafe python3-matplotlib
python3-minimal python3-nose python3-numpy python3-packaging python3-pandas
python3-pandas-lib python3-pkg-resources python3-pygments python3-pyparsing
python3-requests python3-roman python3-scipy python3-setuptools python3-six
python3-sphinx python3-tz python3-urllib3 python3.8 python3.8-dev
python3.8-minimal sgml-base sphinx-common ttf-bitstream-vera xml-core
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-10-locales cython-doc
dh-make gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev groff
libjs-jquery-ui-docs libstdc++-10-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python-cycler-doc
docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-future-doc
python-h5py-doc python-jinja2-doc dvipng ffmpeg ghostscript gir1.2-gtk-3.0
inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi
python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip
python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft
python-nose-doc gfortran python-numpy-doc python3-pytest python3-numpy-dbg
python-pandas-doc python3-statsmodels python-pygments-doc
python-pyparsing-doc python3-cryptography python3-openssl python3-socks
python-requests-doc python-scipy-doc python-setuptools-doc
fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax
python3-sphinx-rtd-theme python3-stemmer sphinx-doc
texlive-fonts-recommended texlive-plain-generic python3.8-venv python3.8-doc
binfmt-support sgml-base-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common libltdl-dev libmail-sendmail-perl
libpaper-utils python3-pil python3-tk python3-bottleneck python3-numexpr
python3-odf python3-openpyxl python3-xlrd python3-xlwt python3-bs4
python3-html5lib python3-lxml python3-tables
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bash-completion ca-certificates
cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism
docutils-common dwz file fonts-lyx gettext gettext-base groff-base help2man
intltool-debian libaec0 libarchive-zip-perl libblas3 libbrotli1 libcroco3
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfreetype6 libgfortran5 libglib2.0-0
libhdf5-103-1 libhdf5-hl-100 libicu67 libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libmagic-mgc
libmagic1 libpipeline1 libpng16-16 libpython3-all-dev libpython3-dev
libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libssl1.1 libsub-override-perl libsz2
libtool libuchardet0 libxml2 m4 man-db mime-support node-jquery openssl
po-debconf python-babel-localedata python-matplotlib-data python3
python3-alabaster python3-all python3-all-dev python3-babel python3-certifi
python3-chardet python3-click python3-colorama python3-cycler
python3-dateutil python3-decorator python3-dev python3-distutils
python3-docutils python3-future python3-h5py python3-h5py-serial
python3-idna python3-imagesize python3-jinja2 python3-kiwisolver
python3-lib2to3 python3-markupsafe python3-matplotlib python3-minimal
python3-nose python3-numpy python3-packaging python3-pandas
python3-pandas-lib python3-pkg-resources python3-pygments python3-pyparsing
python3-requests python3-roman python3-scipy python3-setuptools python3-six
python3-sphinx python3-tz python3-urllib3 python3.8 python3.8-dev
python3.8-minimal sbuild-build-depends-python-biom-format-dummy sgml-base
sphinx-common ttf-bitstream-vera xml-core zlib1g-dev
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base libasan6 libatomic1 libcc1-0 libgcc-10-dev
libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
13 upgraded, 120 newly installed, 0 to remove and 33 not upgraded.
Need to get 103 MB/104 MB of archives.
After this operation, 305 MB of additional disk space will be used.
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Get:2 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-5+rpi1 [31.7 kB]
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Get:16 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.5-2 [752 kB]
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Get:32 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
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Get:34 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
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Get:38 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
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Get:42 http://172.17.0.1/private bullseye-staging/main armhf cython3 armhf 0.29.21-1 [1318 kB]
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Get:53 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
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Get:56 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
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Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1184 kB]
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Get:77 http://172.17.0.1/private bullseye-staging/main armhf node-jquery all 3.5.1+dfsg-4 [309 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.5.1+dfsg-4 [3612 B]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libjs-sphinxdoc all 3.2.1-1 [122 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.3-9 [24.6 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf liblzf1 armhf 3.6-2 [9092 B]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8 armhf 3.8.5-2 [1363 kB]
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Get:89 http://172.17.0.1/private bullseye-staging/main armhf python-babel-localedata all 2.8.0+dfsg.1-4 [4996 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf ttf-bitstream-vera all 1.10-8 [352 kB]
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Get:94 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf python3.8-dev armhf 3.8.5-2 [515 kB]
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Get:97 http://172.17.0.1/private bullseye-staging/main armhf python3-all-dev armhf 3.8.2-3 [1064 B]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 46.1.3-1 [183 kB]
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Get:105 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.15.0-1 [16.8 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf python3-cycler all 0.10.0-3 [8084 B]
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Get:109 http://172.17.0.1/private bullseye-staging/main armhf python3-roman all 2.0.0-5 [9064 B]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python3-docutils all 0.16+dfsg-3 [384 kB]
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Get:112 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.18.4-1 [3037 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf python3-h5py-serial armhf 2.10.0-9 [596 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf python3-h5py all 2.10.0-9 [11.4 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf python3-idna all 2.10-1 [37.4 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf python3-imagesize all 1.2.0-2 [5824 B]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf python3-markupsafe armhf 1.1.1-1 [15.0 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf python3-jinja2 all 2.11.2-1 [113 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf python3-kiwisolver armhf 1.0.1-3 [245 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.7-1 [109 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf python3-matplotlib armhf 3.2.2-1 [4620 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf python3-nose all 1.3.7-7 [133 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 20.4-1 [30.4 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf python3-pandas-lib armhf 1.0.5+dfsg-3+rpi1 [2841 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf python3-pandas all 1.0.5+dfsg-3+rpi1 [1982 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf python3-pygments all 2.3.1+dfsg-4 [596 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf python3-urllib3 all 1.25.9-1 [105 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf python3-requests all 2.23.0+dfsg-2 [71.4 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf python3-scipy armhf 1.4.1-2 [10.4 MB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 46.1.3-1 [382 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf sphinx-common all 3.2.1-1 [574 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf python3-sphinx all 3.2.1-1 [534 kB]
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up ttf-bitstream-vera (1.10-8) ...
Setting up mime-support (3.64) ...
Setting up libicu67:armhf (67.1-4) ...
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Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.4-1) ...
No schema files found: doing nothing.
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Setting up file (1:5.38-5) ...
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Setting up python-babel-localedata (2.8.0+dfsg.1-4) ...
Setting up libasan6:armhf (10.2.0-5+rpi1) ...
Setting up help2man (1.47.16) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-3) ...
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 libexpat1-dev:armhf (2.2.9-1) ...
Setting up bash-completion (1:2.11-2) ...
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Setting up libatomic1:armhf (10.2.0-5+rpi1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libgfortran5:armhf (10.2.0-5+rpi1) ...
Setting up libubsan1:armhf (10.2.0-5+rpi1) ...
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Setting up sgml-base (1.30) ...
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Setting up libjs-underscore (1.9.1~dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
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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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Setting up python3-six (1.15.0-1) ...
Setting up ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
126 added, 0 removed; done.
Setting up python3-roman (2.0.0-5) ...
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Setting up python3-pyparsing (2.4.7-1) ...
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Setting up cython3 (0.29.21-1) ...
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Setting up gcc-10 (10.2.0-5+rpi1) ...
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Setting up libjs-jquery (3.5.1+dfsg-4) ...
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Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up gettext (0.19.8.1-10) ...
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Setting up python3-setuptools (46.1.3-1) ...
Setting up python3-babel (2.8.0+dfsg.1-4) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-colorama (0.4.3-1) ...
Setting up python3-alabaster (0.7.8-1.1) ...
Setting up python3-all (3.8.2-3) ...
Setting up python3-click (7.0-3) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3-nose (1.3.7-7) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up python3-pygments (2.3.1+dfsg-4) ...
Setting up python3-packaging (20.4-1) ...
Setting up python3-chardet (3.0.4-7) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-5) ...
Setting up libpython3.8-dev:armhf (3.8.5-2) ...
Setting up python3-requests (2.23.0+dfsg-2) ...
Setting up python3-kiwisolver (1.0.1-3) ...
Setting up python3-numpy (1:1.18.4-1) ...
Setting up libjs-sphinxdoc (3.2.1-1) ...
Setting up python3.8-dev (3.8.5-2) ...
Setting up python3-future (0.18.2-4) ...
update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode
update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode
Setting up python3-matplotlib (3.2.2-1) ...
Setting up python3-scipy (1.4.1-2) ...
Setting up libpython3-dev:armhf (3.8.2-3) ...
Setting up po-debconf (1.0.21) ...
Setting up python3-pandas-lib:armhf (1.0.5+dfsg-3+rpi1) ...
Setting up python3-h5py-serial (2.10.0-9) ...
Setting up python3-pandas (1.0.5+dfsg-3+rpi1) ...
Setting up libpython3-all-dev:armhf (3.8.2-3) ...
Setting up sphinx-common (3.2.1-1) ...
Setting up python3-dev (3.8.2-3) ...
Setting up python3-h5py (2.10.0-9) ...
Setting up python3-all-dev (3.8.2-3) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Processing triggers for libc-bin (2.31-3+rpi1) ...
Processing triggers for sgml-base (1.30) ...
Setting up docutils-common (0.16+dfsg-3) ...
Processing triggers for sgml-base (1.30) ...
Setting up python3-docutils (0.16+dfsg-3) ...
update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up python3-sphinx (3.2.1-1) ...
Setting up sbuild-build-depends-python-biom-format-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20200601) ...
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.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35-1+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-5+rpi1 gcc-10_10.2.0-5+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-1+b1 aptitude-common_0.8.13-1 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 bash-completion_1:2.11-2 binutils_2.35-1+rpi1 binutils-arm-linux-gnueabihf_2.35-1+rpi1 binutils-common_2.35-1+rpi1 bsdextrautils_2.36-2 bsdutils_1:2.36-2 build-essential_12.8 bzip2_1.0.8-4 ca-certificates_20200601 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-5+rpi1 cython3_0.29.21-1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 docutils-common_0.16+dfsg-3 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-2 file_1:5.38-5 findutils_4.7.0-1 fonts-lyx_2.3.5.2-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-5+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-5+rpi1 gcc-10-base_10.2.0-5+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.16 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libaec0_1.0.4-1 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-5+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-5+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35-1+rpi1 libblas3_3.9.0-3 libblkid1_2.36-2 libboost-iostreams1.71.0_1.71.0-6+b1 libbrotli1_1.0.7-7 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-5+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.35-1+rpi1 libctf0_2.35-1+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdpkg-perl_1.20.5+rpi1 libelf1_0.180-1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-2 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libfreetype6_2.10.2+dfsg-3 libgcc-10-dev_10.2.0-5+rpi1 libgcc-s1_10.2.0-5+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10.2.0-5+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-5+rpi1 libgpg-error0_1.38-2 libhdf5-103-1_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjs-jquery_3.5.1+dfsg-4 libjs-jquery-ui_1.12.1+dfsg-5 libjs-sphinxdoc_3.2.1-1 libjs-underscore_1.9.1~dfsg-1 libksba8_1.4.0-2 liblapack3_3.9.0-3 liblbfgsb0_3.0+dfsg.3-9 libldap-2.4-2_2.4.50+dfsg-1+b1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzf1_3.6-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 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_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpng16-16_1.6.37-2 libpython3-all-dev_3.8.2-3 libpython3-dev_3.8.2-3 libpython3-stdlib_3.8.2-3 libpython3.8_3.8.5-2 libpython3.8-dev_3.8.5-2 libpython3.8-minimal_3.8.5-2 libpython3.8-stdlib_3.8.5-2 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-2 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1+b1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1+b1 libunistring2_0.9.10-4 libuuid1_2.36-2 libxapian30_1.4.15-1 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 node-jquery_3.5.1+dfsg-4 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 python-babel-localedata_2.8.0+dfsg.1-4 python-matplotlib-data_3.2.2-1 python3_3.8.2-3 python3-alabaster_0.7.8-1.1 python3-all_3.8.2-3 python3-all-dev_3.8.2-3 python3-babel_2.8.0+dfsg.1-4 python3-certifi_2020.4.5.1-1 python3-chardet_3.0.4-7 python3-click_7.0-3 python3-colorama_0.4.3-1 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-4 python3-decorator_4.4.2-2 python3-dev_3.8.2-3 python3-distutils_3.8.5-1 python3-docutils_0.16+dfsg-3 python3-future_0.18.2-4 python3-h5py_2.10.0-9 python3-h5py-serial_2.10.0-9 python3-idna_2.10-1 python3-imagesize_1.2.0-2 python3-jinja2_2.11.2-1 python3-kiwisolver_1.0.1-3 python3-lib2to3_3.8.5-1 python3-markupsafe_1.1.1-1 python3-matplotlib_3.2.2-1 python3-minimal_3.8.2-3 python3-nose_1.3.7-7 python3-numpy_1:1.18.4-1 python3-packaging_20.4-1 python3-pandas_1.0.5+dfsg-3+rpi1 python3-pandas-lib_1.0.5+dfsg-3+rpi1 python3-pkg-resources_46.1.3-1 python3-pygments_2.3.1+dfsg-4 python3-pyparsing_2.4.7-1 python3-requests_2.23.0+dfsg-2 python3-roman_2.0.0-5 python3-scipy_1.4.1-2 python3-setuptools_46.1.3-1 python3-six_1.15.0-1 python3-sphinx_3.2.1-1 python3-tz_2020.1-2 python3-urllib3_1.25.9-1 python3.8_3.8.5-2 python3.8-dev_3.8.5-2 python3.8-minimal_3.8.5-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-biom-format-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.30 sphinx-common_3.2.1-1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 ttf-bitstream-vera_1.10-8 tzdata_2020a-1 util-linux_2.36-2 xml-core_0.18+nmu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Q_TjUGyd/trustedkeys.kbx': General error
gpgv: Signature made Sun Jul 19 11:49:20 2020 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-biom-format_2.1.8+dfsg-3.dsc
dpkg-source: info: extracting python-biom-format in /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg
dpkg-source: info: unpacking python-biom-format_2.1.8+dfsg.orig.tar.xz
dpkg-source: info: unpacking python-biom-format_2.1.8+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying ignore_local_dist-packages.patch
dpkg-source: info: applying no-web-adds.patch
dpkg-source: info: applying fix_future_import.patch
dpkg-source: info: applying enable_sloppy_sphinx_build.patch
dpkg-source: info: applying sphinx_1.6.patch
dpkg-source: info: applying sphinx.ext.pngmath.patch
dpkg-source: info: applying posix_shell.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.1.8+dfsg-3+b1
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-d4a24d84-278f-43ac-93bc-8ea0925c092e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package python-biom-format
dpkg-buildpackage: info: source version 2.1.8+dfsg-3+b1
dpkg-buildpackage: info: source distribution bullseye-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3,bash-completion,sphinxdoc --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
install -d /<<BUILDDIR>>/python-biom-format-2.1.8\+dfsg/debian/.debhelper/generated/_source/home
pybuild --clean --test-nose -i python{version} -p 3.8
I: pybuild base:217: python3.8 setup.py clean
Compiling biom/_filter.pyx because it changed.
Compiling biom/_transform.pyx because it changed.
Compiling biom/_subsample.pyx because it changed.
[1/3] Cythonizing biom/_filter.pyx
[2/3] Cythonizing biom/_subsample.pyx
[3/3] Cythonizing biom/_transform.pyx
running clean
removing '/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build' (and everything under it)
/usr/lib/python3/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-biom-format-2.1.8+dfsg/biom/_filter.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/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-biom-format-2.1.8+dfsg/biom/_subsample.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/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-biom-format-2.1.8+dfsg/biom/_transform.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.8' does not exist -- can't clean it
rm -rf .pybuild/
find . -name \*.pyc -exec rm {} \;
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/python3-biom-format.substvars debian/python-biom-format-doc.substvars ./biom/_filter.c ./biom/_subsample.c ./biom/_transform.c debian/files
rm -fr -- debian/python3-biom-format/ debian/tmp/ debian/python-biom-format-doc/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary-arch
dh binary-arch --with python3,bash-completion,sphinxdoc --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
install -d /<<BUILDDIR>>/python-biom-format-2.1.8\+dfsg/debian/.debhelper/generated/_source/home
pybuild --configure --test-nose -i python{version} -p 3.8
I: pybuild base:217: python3.8 setup.py config
Compiling biom/_filter.pyx because it changed.
Compiling biom/_transform.pyx because it changed.
Compiling biom/_subsample.pyx because it changed.
[1/3] Cythonizing biom/_filter.pyx
[2/3] Cythonizing biom/_subsample.pyx
[3/3] Cythonizing biom/_transform.pyx
running config
/usr/lib/python3/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-biom-format-2.1.8+dfsg/biom/_filter.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/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-biom-format-2.1.8+dfsg/biom/_subsample.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/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-biom-format-2.1.8+dfsg/biom/_transform.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg'
# arch
USE_CYTHON=true dh_auto_build
pybuild --build --test-nose -i python{version} -p 3.8
I: pybuild base:217: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/err.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/exception.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/parse.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/table.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/util.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/__init__.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/__init__.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/installation_informer.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/metadata_adder.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/metadata_exporter.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_converter.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_head.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_ids.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_normalizer.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_subsetter.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_summarizer.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/table_validator.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/uc_processor.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
copying biom/cli/util.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
copying biom/tests/__init__.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
copying biom/tests/long_lines.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
copying biom/tests/test_err.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
copying biom/tests/test_parse.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
copying biom/tests/test_table.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
copying biom/tests/test_util.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/__init__.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_add_metadata.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_show_install_info.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_subset_table.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_summarize_table.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_table_converter.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_table_normalizer.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_uc_processor.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
copying biom/tests/test_cli/test_validate_table.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/__init__.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
running egg_info
creating biom_format.egg-info
writing biom_format.egg-info/PKG-INFO
writing dependency_links to biom_format.egg-info/dependency_links.txt
writing entry points to biom_format.egg-info/entry_points.txt
writing requirements to biom_format.egg-info/requires.txt
writing top-level names to biom_format.egg-info/top_level.txt
writing manifest file 'biom_format.egg-info/SOURCES.txt'
reading manifest file 'biom_format.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'support_files'
warning: no directories found matching 'tests/test_data'
no previously-included directories found matching 'docs/_build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '.*.swp' found anywhere in distribution
writing manifest file 'biom_format.egg-info/SOURCES.txt'
copying biom/_filter.c -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/_filter.pyx -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/_subsample.c -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/_subsample.pyx -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/_transform.c -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
copying biom/_transform.pyx -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/assets
copying biom/assets/exercise_api.py -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/assets
copying biom/assets/exercise_cli.sh -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/assets
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
creating /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
copying biom/tests/test_cli/test_data/test.biom -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
copying biom/tests/test_cli/test_data/test.json -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
copying biom/tests/test_data/bad_table.txt -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/bad_table.txt.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/empty.biom -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/no-contents.biom -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/test.biom -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/test.json -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/test.json.gz -> /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
running build_ext
building 'biom._filter' extension
creating build
creating build/temp.linux-armhf-3.8
creating build/temp.linux-armhf-3.8/biom
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c biom/_filter.c -o build/temp.linux-armhf-3.8/biom/_filter.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from biom/_filter.c:629:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/biom/_filter.o -o /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/_filter.cpython-38-arm-linux-gnueabihf.so
building 'biom._transform' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c biom/_transform.c -o build/temp.linux-armhf-3.8/biom/_transform.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from biom/_transform.c:629:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/biom/_transform.o -o /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/_transform.cpython-38-arm-linux-gnueabihf.so
building 'biom._subsample' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c biom/_subsample.c -o build/temp.linux-armhf-3.8/biom/_subsample.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from biom/_subsample.c:629:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/biom/_subsample.o -o /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/_subsample.cpython-38-arm-linux-gnueabihf.so
# indep:
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
Running Sphinx v3.2.1
making output directory... done
[autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst
Failed to import 'biom': no module named biom
Failed to import 'biom.table': no module named biom.table
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 12 source files that are out of date
updating environment: [new config] 12 added, 0 changed, 0 removed
reading sources... [ 8%] BIOM_LICENSE
reading sources... [ 16%] documentation/adding_metadata
reading sources... [ 25%] documentation/biom_conversion
reading sources... [ 33%] documentation/biom_format
reading sources... [ 41%] documentation/format_versions/biom-1.0
reading sources... [ 50%] documentation/format_versions/biom-2.0
reading sources... [ 58%] documentation/format_versions/biom-2.1
reading sources... [ 66%] documentation/index
reading sources... [ 75%] documentation/quick_usage_examples
reading sources... [ 83%] documentation/summarizing_biom_tables
reading sources... [ 91%] documentation/table_objects
reading sources... [100%] index
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/doc/conf.py:238: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead.
app.add_javascript('copybutton.js')
WARNING: autodoc: failed to import module 'biom'; the following exception was raised:
No module named 'biom._filter'
WARNING: autodoc: failed to import module 'table' from module 'biom'; the following exception was raised:
No module named 'biom._filter'
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 8%] BIOM_LICENSE
writing output... [ 16%] documentation/adding_metadata
writing output... [ 25%] documentation/biom_conversion
writing output... [ 33%] documentation/biom_format
writing output... [ 41%] documentation/format_versions/biom-1.0
writing output... [ 50%] documentation/format_versions/biom-2.0
writing output... [ 58%] documentation/format_versions/biom-2.1
writing output... [ 66%] documentation/index
writing output... [ 75%] documentation/quick_usage_examples
writing output... [ 83%] documentation/summarizing_biom_tables
writing output... [ 91%] documentation/table_objects
writing output... [100%] index
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated
generating indices... done
writing additional pages... searchdone
copying images... [100%] _static/biom-format.png
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 6 warnings.
The HTML pages are in build/html.
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
Running Sphinx v3.2.1
making output directory... done
[autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst
Failed to import 'biom': no module named biom
Failed to import 'biom.table': no module named biom.table
building [mo]: targets for 0 po files that are out of date
building [man]: all manpages
updating environment: [new config] 12 added, 0 changed, 0 removed
reading sources... [ 8%] BIOM_LICENSE
reading sources... [ 16%] documentation/adding_metadata
reading sources... [ 25%] documentation/biom_conversion
reading sources... [ 33%] documentation/biom_format
reading sources... [ 41%] documentation/format_versions/biom-1.0
reading sources... [ 50%] documentation/format_versions/biom-2.0
reading sources... [ 58%] documentation/format_versions/biom-2.1
reading sources... [ 66%] documentation/index
reading sources... [ 75%] documentation/quick_usage_examples
reading sources... [ 83%] documentation/summarizing_biom_tables
reading sources... [ 91%] documentation/table_objects
reading sources... [100%] index
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/doc/conf.py:238: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead.
app.add_javascript('copybutton.js')
WARNING: autodoc: failed to import module 'biom'; the following exception was raised:
No module named 'biom._filter'
WARNING: autodoc: failed to import module 'table' from module 'biom'; the following exception was raised:
No module named 'biom._filter'
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
writing... biom.1 { documentation/index documentation/biom_format documentation/format_versions/biom-1.0 documentation/format_versions/biom-2.0 documentation/format_versions/biom-2.1 documentation/quick_usage_examples documentation/table_objects documentation/biom_conversion documentation/adding_metadata documentation/summarizing_biom_tables BIOM_LICENSE } done
build succeeded, 2 warnings.
The manual pages are in build/man.
make[1]: Leaving directory '/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg'
dh_auto_test -a -O--buildsystem=pybuild
pybuild --test --test-nose -i python{version} -p 3.8
I: pybuild pybuild:284: cp -r /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/examples /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build
I: pybuild base:217: cd /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build; python3.8 -m nose -v
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:20: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
import pandas.util.testing as pdt
Correctly adds observation metadata without casting it. ... ok
Correctly adds observation metadata with casting. ... ok
Correctly adds sample metadata without casting it. ... ok
Correctly adds sample metadata with casting. ... ok
test_default (biom.tests.test_cli.test_show_install_info.TestShowInstallInfo) ... ok
Correctly raises politically correct error upon invalid input. ... ok
Correctly subsets observations in a table. ... ok
Correctly subsets samples in a hdf5 table ... /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3980: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
data = np.hstack(h5_data[start:end]
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3982: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
indices = np.hstack(h5_indices[start:end]
ok
Correctly subsets samples in a table. ... ok
Correctly subsets samples in a hdf5 table ... ok
TableSummarizer functions as expected ... ok
TableSummarizer functions as expected with qualitative=True ... ok
Correctly converts biom to classic. ... ok
Correctly converts biom to classic with metadata renaming. ... ok
Correctly converts classic to biom. ... ok
Correctly converts classic to biom with metadata. ... ok
Correctly converts json to HDF5 changing the observation metadata ... ok
Correctly converts json to HDF5 changing the sample metadata ... ok
test_bad_inputs (biom.tests.test_cli.test_table_normalizer.TableNormalizerTests) ... ok
test_basic (biom.tests.test_cli.test_uc_processor.TestUcProcessor) ... ok
test_basic_w_mapping (biom.tests.test_cli.test_uc_processor.TestUcProcessor) ... ok
test_rep_set_missing_id (biom.tests.test_cli.test_uc_processor.TestUcProcessor) ... ok
test_rep_set_no_mapping (biom.tests.test_cli.test_uc_processor.TestUcProcessor) ... ok
test_uc (biom.tests.test_cli.test_uc_processor.TestUcProcessor) ... ok
test_uc_w_mapping (biom.tests.test_cli.test_uc_processor.TestUcProcessor) ... ok
Correctly invalidates a table that is... invalid. ... ok
Test an invalid HDF5 table ... ok
test_is_int (biom.tests.test_cli.test_validate_table.TableValidatorTests) ... ok
Correctly validates a table that is indeed... valid. ... ok
validates table:columns: fields ... ok
validates data: fields ... ok
Make sure we have a datetime stamp ... ok
Takes a dense matrix field and validates ... ok
Should match format string ... ok
validates format url ... ok
Should have some string for generated by ... ok
Test a valid HDF5 table ... ok
test_valid_hdf5_metadata_v200 (biom.tests.test_cli.test_validate_table.TableValidatorTests) ... ok
test_valid_hdf5_metadata_v210 (biom.tests.test_cli.test_validate_table.TableValidatorTests) ... ok
Make sure we have a valid matrix type ... ok
Make sure we have a valid matrix type ... ok
Can be nullable or an object ... ok
Should just work. ... ok
validates rows: field ... ok
validates shape information ... ok
Takes a sparse matrix field and validates ... ok
Should be valid table type ... ok
test_test_empty (biom.tests.test_err.ErrModeTests) ... ok
test_test_obsdup (biom.tests.test_err.ErrModeTests) ... ok
test_test_obsmdsize (biom.tests.test_err.ErrModeTests) ... ok
test_test_obssize (biom.tests.test_err.ErrModeTests) ... ok
test_test_sampdup (biom.tests.test_err.ErrModeTests) ... ok
test_test_sampmdsize (biom.tests.test_err.ErrModeTests) ... ok
test_test_sampsize (biom.tests.test_err.ErrModeTests) ... ok
test_contains (biom.tests.test_err.ErrorProfileTests) ... ok
test_getcall (biom.tests.test_err.ErrorProfileTests) ... ok
test_handle_error (biom.tests.test_err.ErrorProfileTests) ... ok
test_register_unregister (biom.tests.test_err.ErrorProfileTests) ... ok
test_setcall (biom.tests.test_err.ErrorProfileTests) ... ok
test_state (biom.tests.test_err.ErrorProfileTests) ... ok
test_test (biom.tests.test_err.ErrorProfileTests) ... ok
test_test_evaluation_order (biom.tests.test_err.ErrorProfileTests) ... ok
test_errcheck (biom.tests.test_err.SupportTests) ... ok
test_errstate (biom.tests.test_err.SupportTests) ... ok
test_geterr (biom.tests.test_err.SupportTests) ... ok
test_geterrcall (biom.tests.test_err.SupportTests) ... ok
test_seterr (biom.tests.test_err.SupportTests) ... ok
test_seterrcall (biom.tests.test_err.SupportTests) ... ok
test_empty_metadata_inconsistent_handling (biom.tests.test_parse.ParseTests) ... ok
get a generatedby string ... ok
test_load_table_filepath (biom.tests.test_parse.ParseTests) ... ok
test_load_table_inmemory (biom.tests.test_parse.ParseTests) ... ok
test_load_table_inmemory_json (biom.tests.test_parse.ParseTests) ... ok
test_load_table_inmemory_stringio (biom.tests.test_parse.ParseTests) ... ok
MetadataMap functions as expected ... ok
MetadataMap functions as expected w user-provided header ... ok
MetadataMap functions as expected w process_fns ... ok
test the biom otu table parser ... ok
tests for parse_biom_table when we do not have h5py ... ok
Make sure we can parse a HDF5 table through the same loader ... ok
test the biom table parser subsetting ... ok
tests for parse_biom_table when we have h5py ... ok
empty uc file returns empty Table ... ok
invalid query sequence identifier detected ... ok
single library seed observed ... ok
single new seed observed ... ok
new and library seeds observed ... ok
multiple new seeds observed ... ok
sample id with underscores is correctly processed ... ok
Yield tables binned by observation metadata ... ok
Yield tables binned by sample metadata ... ok
test_collapse_median (biom.tests.test_table.SparseTableTests) ... ok
Collapse observations by arbitrary metadata ... ok
Collapse observations by arbitary metadata ... ok
Collapse observations by 1-M metadata using divide mode ... ok
Collapse observations by arbitary metadata ... ok
Collapse samples by arbitrary metadata ... ok
Collapse samples by arbitary metadata ... ok
Collapse samples by 1-M metadata using divide mode ... ok
Collapse samples by arbitary metadata ... ok
Should convert other to sparse type ... ok
test_copy_data (biom.tests.test_table.SparseTableTests) ... ok
test_copy_ids (biom.tests.test_table.SparseTableTests) ... ok
test_copy_metadata (biom.tests.test_table.SparseTableTests) ... ok
test_data (biom.tests.test_table.SparseTableTests) ... ok
check equality between tables ... ok
test_data_sparse (biom.tests.test_table.SparseTableTests) ... ok
Print out self in a delimited form ... ok
sparse equality ... ok
Parses a classic table ... ok
test_extract_data_from_tsv_bad_metadata (biom.tests.test_table.SparseTableTests) ... ok
test_extract_data_from_tsv_badvalue_complaint (biom.tests.test_table.SparseTableTests) ... ok
test_filter_general_observation (biom.tests.test_table.SparseTableTests) ... ok
test_filter_general_sample (biom.tests.test_table.SparseTableTests) ... ok
test_filter_id_state (biom.tests.test_table.SparseTableTests) ... ok
test_filter_observations_id (biom.tests.test_table.SparseTableTests) ... ok
test_filter_observations_invert (biom.tests.test_table.SparseTableTests) ... ok
test_filter_observations_metadata (biom.tests.test_table.SparseTableTests) ... ok
test_filter_observations_remove_everything (biom.tests.test_table.SparseTableTests) ... ok
test_filter_out_full_table (biom.tests.test_table.SparseTableTests) ... ok
test_filter_return_type (biom.tests.test_table.SparseTableTests) ... ok
test_filter_sample_id (biom.tests.test_table.SparseTableTests) ... ok
test_filter_sample_invert (biom.tests.test_table.SparseTableTests) ... ok
test_filter_sample_metadata (biom.tests.test_table.SparseTableTests) ... ok
test_filter_sample_remove_everything (biom.tests.test_table.SparseTableTests) ... ok
test_filter_table_with_zeros (biom.tests.test_table.SparseTableTests) ... ok
test_filter_using_list_of_ids (biom.tests.test_table.SparseTableTests) ... ok
test_from_json_issue_697 (biom.tests.test_table.SparseTableTests) ... ok
Test correctly computes density of table. ... ok
test_identify_bad_value (biom.tests.test_table.SparseTableTests) ... ok
Should iterate over samples ... ok
test_iter_data_dense (biom.tests.test_table.SparseTableTests) ... ok
test_iter_data_sparse (biom.tests.test_table.SparseTableTests) ... ok
Iterate over observations of sparse matrix ... ok
Iterates data by observations ... ok
Iterates data by observations from a single sample. ... ok
Iterates observations ... ok
Should iterate pairwise over samples ... ok
Should iterate pairwise over samples ... ok
Should iterate pairwise over samples ... ok
Should iterate pairwise over samples ... ok
Iterate over samples of sparse matrix ... ok
Iterates data by samples ... ok
Iterates data by samples with a single observation. ... ok
Iterates samples ... ok
Merge two tables ... ok
Return a list of nonzero positions ... ok
Returns nonzero counts over an axis ... ok
Returns nonzero counts over an axis ... ok
test_nonzero_csc_bug (biom.tests.test_table.SparseTableTests) ... ok
normalize observations by sample ... ok
normalize sample by observation ... ok
test_other_spmatrix_type (biom.tests.test_table.SparseTableTests) ... ok
test_pa (biom.tests.test_table.SparseTableTests) ... ok
test_pa_with_neg (biom.tests.test_table.SparseTableTests) ... ok
test_pa_works_if_something_has_been_zeroed (biom.tests.test_table.SparseTableTests) ... ok
rank observations by sample ... ok
rank observations by sample with alt method ... ok
rank samples by observation ... ok
Reduce method ... ok
table sorted by a function and provided axis ... ok
sorts tables by arbitrary order ... ok
test_subsample (biom.tests.test_table.SparseTableTests) ... ok
test_subsample_by_id (biom.tests.test_table.SparseTableTests) ... ok
test_subsample_by_id_observations_bug (biom.tests.test_table.SparseTableTests) ... ok
test_subsample_byid_with_replacement (biom.tests.test_table.SparseTableTests) ... ok
subsample would except when if metadata were present ... ok
test_subsample_with_replacement_n (biom.tests.test_table.SparseTableTests) ... ok
As in scikit-bio. Given a vector of observations, the total number of ... ok
As in scikit-bio. Given a vector of observations, the total number of ... ok
Test of sum! ... ok
Should convert a self styled vector to numpy type ... ok
Get a BIOM format string for a dense table of floats ... ok
Get a BIOM format string for a dense table of floats ... ok
Get a BIOM format string for a dense table of integers ... ok
Get a BIOM format string for a dense table of integers ... ok
test_to_json_empty (biom.tests.test_table.SparseTableTests) ... ok
Get a BIOM format string for a sparse table of floats ... ok
Get a BIOM format string for a sparse table of floats ... ok
Get a BIOM format string for a sparse table of integers ... ok
Get a BIOM format string for a sparse table of integers ... ok
Transform axis by arbitrary function ... ok
test_transform_return_type (biom.tests.test_table.SparseTableTests) ... ok
test_transform_sample (biom.tests.test_table.SparseTableTests) ... ok
Should transpose a sparse table ... ok
ids are updated as expected ... ok
test_update_ids_cache_bug (biom.tests.test_table.SparseTableTests) ... ok
ids are updated as expected ... ok
test_align_to_no_overlap (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_autodetect_both (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_autodetect_observation (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_autodetect_sample (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_autodetect_vary_values (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_both (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_both_no_overlap (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_observation (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_observation_no_overlap (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_sample (biom.tests.test_table.SupportTests) ... ok
test_align_to_overlap_sample_no_overlap (biom.tests.test_table.SupportTests) ... ok
test_concat_different_order (biom.tests.test_table.SupportTests) ... ok
test_concat_empty (biom.tests.test_table.SupportTests) ... ok
test_concat_multiple (biom.tests.test_table.SupportTests) ... ok
test_concat_no_metadata_bug (biom.tests.test_table.SupportTests) ... ok
test_concat_observations (biom.tests.test_table.SupportTests) ... ok
test_concat_pad_on_subset (biom.tests.test_table.SupportTests) ... ok
test_concat_raise_overlap (biom.tests.test_table.SupportTests) ... ok
test_concat_samples (biom.tests.test_table.SupportTests) ... ok
test_concat_table_type (biom.tests.test_table.SupportTests) ... ok
test_head (biom.tests.test_table.SupportTests) ... ok
test_head_bounded (biom.tests.test_table.SupportTests) ... ok
test_head_overstep (biom.tests.test_table.SupportTests) ... ok
test_head_zero_or_neg (biom.tests.test_table.SupportTests) ... ok
returns a dict for list lookups ... ok
prefer x ... ok
test_remove_empty_both (biom.tests.test_table.SupportTests) ... /usr/lib/python3/dist-packages/scipy/sparse/_index.py:126: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient.
self._set_arrayXarray(i, j, x)
ok
test_remove_empty_identity (biom.tests.test_table.SupportTests) ... ok
test_remove_empty_obs (biom.tests.test_table.SupportTests) ... ok
test_remove_empty_sample (biom.tests.test_table.SupportTests) ... ok
Make sure a TableException can be raised ... ok
beat the table sparsely to death ... ok
beat the table sparsely to death ... ok
beat the table sparsely to death ... ok
beat the table sparsely to death ... ok
beat the table sparsely to death ... ok
convert (values, (row, col)) to scipy ... ok
Take a dict and convert to sparse ... ok
Take a list of dicts and condense down to a single dict ... ok
convert [[row,col,value], ...] to scipy ... ok
lists of nparrays to sparse ... ok
list of lil_matrix to sparse ... ok
Convert nparray to sparse ... ok
Convert to expected sparse types ... ok
add group metadata works correctly ... ok
add group metadata works with existing metadata ... ok
add_sample_metadata functions with single md entry ... ok
add_sample_metadata functions with existing metadata ... ok
add_metadata functions with more than one md entry ... ok
add_sample_metadata functions with more than one md entry ... ok
test_all_keys_dropped (biom.tests.test_table.TableTests) ... ok
Cast metadata objects to defaultdict to support default values ... ok
Properly converts ScipySparseMat vectors to dense numpy repr. ... ok
test_data_property (biom.tests.test_table.TableTests) ... ok
test_del_metadata_badaxis (biom.tests.test_table.TableTests) ... ok
test_del_metadata_defaults (biom.tests.test_table.TableTests) ... ok
test_del_metadata_empty_list (biom.tests.test_table.TableTests) ... ok
test_del_metadata_full (biom.tests.test_table.TableTests) ... ok
test_del_metadata_idempotent (biom.tests.test_table.TableTests) ... ok
test_del_metadata_jagged (biom.tests.test_table.TableTests) ... ok
test_del_metadata_keys_none_observation (biom.tests.test_table.TableTests) ... ok
test_del_metadata_keys_none_sample (biom.tests.test_table.TableTests) ... ok
test_del_metadata_keys_none_whole (biom.tests.test_table.TableTests) ... ok
test_del_metadata_multiple_keys (biom.tests.test_table.TableTests) ... ok
test_del_metadata_nomd (biom.tests.test_table.TableTests) ... ok
test_del_metadata_partial (biom.tests.test_table.TableTests) ... ok
What's your type? ... ok
Test whether two matrices are equal. ... ok
Verify ValueError raised! ... ok
Parse a hdf5 formatted BIOM table ... ok
test_from_hdf5_custom_parsers (biom.tests.test_table.TableTests) ... ok
Parse a hdf5 formatted BIOM table w/o metadata ... ok
HDF5 biom parse successfully loads an empty table ... ok
test_from_hdf5_issue_731 (biom.tests.test_table.TableTests) ... ok
test_from_hdf5_non_hdf5_file_or_group (biom.tests.test_table.TableTests) ... ok
Parse a observation subset of a hdf5 formatted BIOM table ... /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3980: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
data = np.hstack(h5_data[start:end]
/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3982: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
indices = np.hstack(h5_indices[start:end]
ok
Parse a observation subset of a hdf5 formatted BIOM table ... ok
Parse a sample subset of a hdf5 formatted BIOM table ... ok
Parse a sample subset of a hdf5 formatted BIOM table ... ok
hdf5 biom table parse throws error with invalid parameters ... ok
test_from_tsv (biom.tests.test_table.TableTests) ... ok
test_from_tsv_dense (biom.tests.test_table.TableTests) ... ok
Test grabbing a column from the matrix. ... ok
Test grabbing a row from the matrix. ... ok
Return the value located in the matrix by the ids ... ok
getitem should work as expeceted ... ok
Test getting an element from the matrix. ... ok
Handles invalid input ... ok
Returns the observation group metadata ... ok
Returns the sample group metadata ... ok
Index all the ids!!! ... ok
Correctly handles invalid input. ... ok
returns the observation index ... ok
returns the sample index ... ok
to_sparse in constructor should be triggered ... ok
Combine ids, intersection ... ok
returns true if empty ... ok
test_length (biom.tests.test_table.TableTests) ... ok
test_max_observation (biom.tests.test_table.TableTests) ... ok
test_max_sample (biom.tests.test_table.TableTests) ... ok
test_max_whole (biom.tests.test_table.TableTests) ... ok
Correctly handles invalid input. ... ok
returns the observation metadata ... ok
returns the observation metadata for a given id ... ok
Return the sample metadata ... ok
returns the sample metadata for a given id ... ok
test_metadata_to_dataframe (biom.tests.test_table.TableTests) ... ok
test_metadata_to_dataframe_badaxis (biom.tests.test_table.TableTests) ... ok
test_metadata_to_dataframe_nomd (biom.tests.test_table.TableTests) ... ok
test_metadata_to_dataframe_uneven_list_metadata (biom.tests.test_table.TableTests) ... ok
test_min_observation (biom.tests.test_table.TableTests) ... ok
test_min_sample (biom.tests.test_table.TableTests) ... ok
test_min_whole (biom.tests.test_table.TableTests) ... ok
Test whether two matrices are not equal. ... ok
What is your NNZ? ... ok
test_nnz_issue_727 (biom.tests.test_table.TableTests) ... /usr/lib/python3/dist-packages/scipy/sparse/_index.py:84: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient.
self._set_intXint(row, col, x.flat[0])
ok
Verify observation exist! ... ok
__repr__ method of biom.table.Table ... ok
Verify samples exist! ... ok
What kind of shape are you in? ... ok
test_to_dataframe (biom.tests.test_table.TableTests) ... /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:1476: FutureWarning: The SparseDataFrame class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version
exp = pd.SparseDataFrame(np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]]),
ERROR
test_to_dataframe_dense (biom.tests.test_table.TableTests) ... ok
test_to_dataframe_is_sparse (biom.tests.test_table.TableTests) ... /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:4049: FutureWarning: The SparseDataFrame class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version
constructor = partial(pd.SparseDataFrame,
ERROR
Write a file ... ok
test_to_hdf5_custom_formatters (biom.tests.test_table.TableTests) ... ok
Successfully writes an empty OTU table in HDF5 format ... ok
Successfully writes an empty OTU table in HDF5 format ... ok
test_to_hdf5_general_fallback_to_list (biom.tests.test_table.TableTests) ... ok
test_to_hdf5_inconsistent_metadata_categories_observation (biom.tests.test_table.TableTests) ... ok
test_to_hdf5_inconsistent_metadata_categories_sample (biom.tests.test_table.TableTests) ... ok
test_to_hdf5_malformed_taxonomy (biom.tests.test_table.TableTests) ... ok
test_to_hdf5_missing_metadata_observation (biom.tests.test_table.TableTests) ... ok
test_to_hdf5_missing_metadata_sample (biom.tests.test_table.TableTests) ... ok
Print out self in a delimited form ... ok
Combine unique ids, union ... ok
Make sure the metadata is sane (including obs/sample ids) ... ok
test_biom_open_empty (biom.tests.test_util.UtilTests) ... ok
test_biom_open_hdf5 (biom.tests.test_util.UtilTests) ... ok
test_biom_open_hdf5_no_h5py (biom.tests.test_util.UtilTests) ... SKIP: Skipping test: test_biom_open_hdf5_no_h5py: Can only be tested without H5PY
test_biom_open_json (biom.tests.test_util.UtilTests) ... ok
compute_counts_per_sample_stats functions as expected ... ok
test_compute_counts_per_sample_stats_empty (biom.tests.test_util.UtilTests) ... ok
compute_counts_per_sample_stats functions as expected ... ok
flatten should remove one level of nesting from nested sequences ... ok
flatten should not change non-nested sequences (except to list) ... ok
test_generate_subsamples (biom.tests.test_util.UtilTests) ... ok
Getting the biom project directory functions as expected. ... ok
test_is_hdf5_file (biom.tests.test_util.UtilTests) ... ok
test_load_classic (biom.tests.test_util.UtilTests) ... ok
test_load_table_gzip_unicode (biom.tests.test_util.UtilTests) ... ok
test_load_table_unicode (biom.tests.test_util.UtilTests) ... ok
natsort should perform numeric comparisons on strings ... ok
parse_biom_config_files functions as expected. ... ok
Make sure we have the expected md5 with varied input types ... ok
unzip(items) should be the inverse of zip(*items) ... ok
======================================================================
ERROR: test_to_dataframe (biom.tests.test_table.TableTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py", line 1476, in test_to_dataframe
exp = pd.SparseDataFrame(np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]]),
TypeError: SparseDataFrame() takes no arguments
======================================================================
ERROR: test_to_dataframe_is_sparse (biom.tests.test_table.TableTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py", line 1484, in test_to_dataframe_is_sparse
df = example_table.to_dataframe()
File "/<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py", line 4053, in to_dataframe
return constructor(mat, index=index, columns=columns)
TypeError: SparseDataFrame() takes no arguments
----------------------------------------------------------------------
Ran 343 tests in 49.533s
FAILED (SKIP=1, errors=2)
E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build; python3.8 -m nose -v
rm -fr -- /tmp/dh-xdg-rundir-6lnSLxQ5
dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13
make: *** [debian/rules:19: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-09-01T16:58:12Z
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: 197
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 869
Job: python-biom-format_2.1.8+dfsg-3
Machine Architecture: armhf
Package: python-biom-format
Package-Time: 1120
Source-Version: 2.1.8+dfsg-3
Space: 0
Status: failed
Version: 2.1.8+dfsg-3+b1
--------------------------------------------------------------------------------
Finished at 2020-09-01T16:58:12Z
Build needed 00:00:00, 0k disc space