https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18342686 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-056 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:46:18 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 5 Jan 12:57:24 ntpdate[1871]: adjust time server 10.211.37.1 offset -0.016203 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18342686 --image-type chroot /home/buildd/filecache-default/9d93b4075e16ce7cfbdf01f21507152b0a173b17 Creating target for build PACKAGEBUILD-18342686 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18342686 Starting target for build PACKAGEBUILD-18342686 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18342686 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18342686 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18342686 Updating target for build PACKAGEBUILD-18342686 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 Packages [938 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted arm64 Packages [1512 B] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [5768 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe arm64 Packages [8504 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse arm64 Packages [122 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [110 kB] Fetched 15.6 MB in 6s (2441 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 93 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 62.3 MB of archives. After this operation, 44.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main arm64 libc6-dev arm64 2.30-0ubuntu3 [2091 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 libc-dev-bin arm64 2.30-0ubuntu3 [64.1 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main arm64 linux-libc-dev arm64 5.3.0-24.26 [1077 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 libisl22 arm64 0.22-2 [536 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 libcc1-0 arm64 9.2.1-21ubuntu1 [46.4 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-aarch64-linux-gnu arm64 2.33.1-6ubuntu3 [2021 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 libbinutils arm64 2.33.1-6ubuntu3 [471 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-common arm64 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 binutils arm64 2.33.1-6ubuntu3 [3392 B] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-9-base arm64 9.2.1-21ubuntu1 [19.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc1 arm64 1:9.2.1-21ubuntu1 [34.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main arm64 libgomp1 arm64 9.2.1-21ubuntu1 [80.5 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main arm64 libitm1 arm64 9.2.1-21ubuntu1 [25.0 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libatomic1 arm64 9.2.1-21ubuntu1 [9168 B] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 libasan5 arm64 9.2.1-21ubuntu1 [365 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 liblsan0 arm64 9.2.1-21ubuntu1 [126 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 libtsan0 arm64 9.2.1-21ubuntu1 [284 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main arm64 libubsan1 arm64 9.2.1-21ubuntu1 [121 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main arm64 g++-9 arm64 9.2.1-21ubuntu1 [9602 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++-9-dev arm64 9.2.1-21ubuntu1 [1674 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc-9-dev arm64 9.2.1-21ubuntu1 [915 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-9 arm64 9.2.1-21ubuntu1 [9017 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 cpp-9 arm64 9.2.1-21ubuntu1 [8396 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++6 arm64 9.2.1-21ubuntu1 [466 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 libc6 arm64 2.30-0ubuntu3 [2273 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 base-files arm64 11ubuntu2 [60.0 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main arm64 debianutils arm64 4.9.1 [85.6 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 bash arm64 5.0-5ubuntu1 [603 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main arm64 bsdutils arm64 1:2.34-0.1ubuntu4 [60.8 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 gzip arm64 1.10-0ubuntu4 [93.0 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 hostname arm64 3.23 [11.1 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 ncurses-bin arm64 6.1+20191019-1ubuntu1 [166 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 libperl5.30 arm64 5.30.0-9 [3764 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 perl arm64 5.30.0-9 [224 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 perl-base arm64 5.30.0-9 [1389 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 bzip2 arm64 1.0.8-2 [33.0 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 libbz2-1.0 arm64 1.0.8-2 [32.9 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main arm64 libblkid1 arm64 2.34-0.1ubuntu4 [129 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main arm64 libuuid1 arm64 2.34-0.1ubuntu4 [20.0 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 libfdisk1 arm64 2.34-0.1ubuntu4 [160 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-8-0 arm64 10.34-7 [170 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main arm64 libselinux1 arm64 3.0-1 [64.8 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main arm64 libmount1 arm64 2.34-0.1ubuntu4 [140 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 libncurses6 arm64 6.1+20191019-1ubuntu1 [91.8 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 libtinfo6 arm64 6.1+20191019-1ubuntu1 [80.4 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 libncursesw6 arm64 6.1+20191019-1ubuntu1 [120 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 libsmartcols1 arm64 2.34-0.1ubuntu4 [93.5 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 fdisk arm64 2.34-0.1ubuntu4 [115 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main arm64 util-linux arm64 2.34-0.1ubuntu4 [984 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main arm64 libdebconfclient0 arm64 0.250ubuntu2 [6260 B] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 base-passwd arm64 3.5.47 [47.0 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main arm64 libc-bin arm64 2.30-0ubuntu3 [502 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 sysvinit-utils arm64 2.96-1ubuntu1 [20.5 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main arm64 liblz4-1 arm64 1.9.2-2 [52.7 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main arm64 systemd-sysv arm64 244-3ubuntu1 [9368 B] Get:59 http://ftpmaster.internal/ubuntu focal/main arm64 libacl1 arm64 2.2.53-5ubuntu1 [17.7 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main arm64 libapparmor1 arm64 2.13.3-7ubuntu1 [33.2 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 libcap-ng0 arm64 0.7.9-2.1 [10.5 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit1 arm64 1:2.8.5-2ubuntu5 [38.4 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main arm64 libcap2 arm64 1:2.27-1 [13.9 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main arm64 libudev1 arm64 244-3ubuntu1 [70.2 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 libdevmapper1.02.1 arm64 2:1.02.155-2ubuntu7 [111 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main arm64 libjson-c4 arm64 0.13.1+dfsg-6 [28.0 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 libcryptsetup12 arm64 2:2.2.2-1ubuntu1 [166 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main arm64 libnettle7 arm64 3.5.1+really3.5.1-2 [124 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main arm64 libhogweed5 arm64 3.5.1+really3.5.1-2 [134 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main arm64 libp11-kit0 arm64 0.23.18.1-2 [177 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main arm64 libtasn1-6 arm64 4.15.0-2 [36.3 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main arm64 libgnutls30 arm64 3.6.11.1-2 [721 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main arm64 libkmod2 arm64 26-3ubuntu1 [39.5 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main arm64 libpam0g arm64 1.3.1-5ubuntu4 [53.9 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main arm64 libseccomp2 arm64 2.4.2-2ubuntu1 [39.9 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main arm64 mount arm64 2.34-0.1ubuntu4 [112 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main arm64 systemd arm64 244-3ubuntu1 [3382 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main arm64 libsystemd0 arm64 244-3ubuntu1 [240 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 libzstd1 arm64 1.4.4+dfsg-1 [216 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main arm64 libapt-pkg5.90 arm64 1.9.5 [776 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libgcrypt20 arm64 1.8.5-3ubuntu1 [350 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 gpgv arm64 2.2.17-3ubuntu1 [183 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 apt arm64 1.9.5 [1231 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-modules-bin arm64 1.3.1-5ubuntu4 [35.8 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-modules arm64 1.3.1-5ubuntu4 [242 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 libattr1 arm64 1:2.4.48-5 [12.5 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 libsepol1 arm64 3.0-1 [231 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage-common all 3.0-1 [9880 B] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage1 arm64 3.0-1 [79.6 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main arm64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main arm64 libsqlite3-0 arm64 3.30.1-1ubuntu1 [499 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main arm64 gpg arm64 2.2.17-3ubuntu1 [437 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main arm64 gpgconf arm64 2.2.17-3ubuntu1 [117 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 gpg-agent arm64 2.2.17-3ubuntu1 [216 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main arm64 liblockfile-bin arm64 1.16-1.1 [11.3 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main arm64 liblockfile1 arm64 1.16-1.1 [6440 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.3 MB in 2s (26.2 MB/s) (Reading database ... 12731 files and directories currently installed.) 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Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up binutils-aarch64-linux-gnu (2.33.1-6ubuntu3) ... Setting up binutils (2.33.1-6ubuntu3) ... Setting up libgcc-9-dev:arm64 (9.2.1-21ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-21ubuntu1) ... Setting up libc6-dev:arm64 (2.30-0ubuntu3) ... Setting up libcryptsetup12:arm64 (2:2.2.2-1ubuntu1) ... Setting up gcc-9 (9.2.1-21ubuntu1) ... Setting up libstdc++-9-dev:arm64 (9.2.1-21ubuntu1) ... Setting up systemd (244-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-21ubuntu1) ... Setting up systemd-sysv (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18342686 arm64 focal -c chroot:build-PACKAGEBUILD-18342686 --arch=arm64 --dist=focal --nolog python-biom-format_2.1.7+dfsg-3ubuntu2.dsc Initiating build PACKAGEBUILD-18342686 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:46:18 UTC 2019 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-056.buildd +==============================================================================+ | python-biom-format 2.1.7+dfsg-3ubuntu2 (arm64) 05 Jan 2020 12:58 | +==============================================================================+ Package: python-biom-format Version: 2.1.7+dfsg-3ubuntu2 Source Version: 2.1.7+dfsg-3ubuntu2 Distribution: focal Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/python-biom-format-LbtPX3/python-biom-format-2.1.7+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biom-format-LbtPX3' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18342686/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biom-format_2.1.7+dfsg-3ubuntu2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-wsrAto/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-wsrAto/apt_archive ./ InRelease Get:2 copy:/<>/resolver-wsrAto/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-wsrAto/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-wsrAto/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-wsrAto/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (40.1 kB/s) Reading package lists... 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-wsrAto/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (75.1 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14649 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), dh-python, cython, 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 Filtered Build-Depends: debhelper-compat (= 12), dh-python, cython, 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 dpkg-deb: building package 'sbuild-build-depends-python-biom-format-dummy' in '/<>/resolver-6Wn1P2/apt_archive/sbuild-build-depends-python-biom-format-dummy.deb'. Ign:1 copy:/<>/resolver-6Wn1P2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-6Wn1P2/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-6Wn1P2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-6Wn1P2/apt_archive ./ Sources [298 B] Get:5 copy:/<>/resolver-6Wn1P2/apt_archive ./ Packages [619 B] Fetched 3036 B in 0s (50.5 kB/s) Reading package lists... 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 packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bash-completion bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base groff-base help2man intltool-debian libaec0 libarchive-zip-perl libblas3 libbsd0 libcroco3 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhdf5-openmpi-103 libhwloc-plugins libhwloc15 libibverbs1 libicu63 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 libmpdec2 libnl-3-200 libnl-route-3-200 libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libsz2 libtool libuchardet0 libxml2 m4 man-db mime-support mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf python-babel-localedata python2 python2-minimal python2.7 python2.7-minimal python3 python3-alabaster python3-all python3-all-dev python3-attr python3-babel python3-certifi python3-chardet python3-click python3-colorama python3-dateutil python3-decorator python3-dev python3-distutils python3-docutils python3-future python3-h5py python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-mpi4py 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 python3.7 python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal sgml-base sphinx-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user pciutils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python2-doc python-tk python2.7-doc binfmt-support python3-doc python3-tk python3-venv python-attr-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 python-nose-doc gfortran python-numpy-doc python3-pytest python3-numpy-dbg python-pandas-doc python3-statsmodels python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-scipy-doc python-setuptools-doc dvipng imagemagick-6.q16 latexmk libjs-mathjax python3-sphinx-rtd-theme python3-stemmer sphinx-doc texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3.7-venv python3.7-doc python3.8-venv python3.8-doc sgml-base-doc Recommended packages: python-dev curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs ibverbs-providers javascript-common krb5-locales libltdl-dev libopenmpi-dev xauth libmail-sendmail-perl libpaper-utils python3-pil python3-matplotlib python3-numexpr python3-tables python3-xlrd python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml The following NEW packages will be installed: autoconf automake autopoint autotools-dev bash-completion bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base groff-base help2man intltool-debian libaec0 libarchive-zip-perl libblas3 libbsd0 libcroco3 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhdf5-openmpi-103 libhwloc-plugins libhwloc15 libibverbs1 libicu63 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 libmpdec2 libnl-3-200 libnl-route-3-200 libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libsz2 libtool libuchardet0 libxml2 m4 man-db mime-support mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf python-babel-localedata python2 python2-minimal python2.7 python2.7-minimal python3 python3-alabaster python3-all python3-all-dev python3-attr python3-babel python3-certifi python3-chardet python3-click python3-colorama python3-dateutil python3-decorator python3-dev python3-distutils python3-docutils python3-future python3-h5py python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-mpi4py 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 python3.7 python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal sbuild-build-depends-python-biom-format-dummy sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 87.8 MB of archives. After this operation, 429 MB of additional disk space will be used. 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libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main arm64 libjs-underscore all 1.9.1~dfsg-1 [98.6 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main arm64 libjs-sphinxdoc all 1.8.5-4 [96.7 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 liblapack3 arm64 3.9.0-1 [1534 kB] Get:97 http://ftpmaster.internal/ubuntu focal/universe arm64 liblbfgsb0 arm64 3.0+dfsg.3-7 [25.5 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.7 arm64 3.7.5-2 [1371 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.7-dev arm64 3.7.5-2 [3048 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3-dev arm64 3.7.5-1ubuntu1 [6940 B] Get:101 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.8-stdlib arm64 3.8.0-5 [1639 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.8 arm64 3.8.0-5 [1485 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.8-dev arm64 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1.1.0-1build1 [14.5 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main arm64 python3-jinja2 all 2.10-2ubuntu2 [95.5 kB] Get:135 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-nose all 1.3.7-4 [116 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pyparsing all 2.4.2-1 [58.8 kB] Get:137 http://ftpmaster.internal/ubuntu focal/main arm64 python3-packaging all 19.1-2 [21.7 kB] Get:138 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-pandas-lib arm64 0.25.3+dfsg-4 [6454 kB] Get:139 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-pandas all 0.25.3+dfsg-4 [1967 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pygments all 2.3.1+dfsg-1ubuntu2 [579 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main arm64 python3-urllib3 all 1.24.1-1ubuntu2 [83.9 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main arm64 python3-requests all 2.21.0-1 [46.8 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main arm64 python3-setuptools all 41.4.0-1 [255 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main arm64 sphinx-common all 1.8.5-4 [492 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main arm64 python3-alabaster all 0.7.8-1build1 [18.7 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main arm64 python3-sphinx all 1.8.5-4 [482 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-scipy arm64 1.3.2-0ubuntu1 [12.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 87.8 MB in 4s (23.0 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Unpacking sbuild-build-depends-python-biom-format-dummy (0.invalid.0) ... Setting up libpipeline1:arm64 (1.5.1-3) ... Setting up libpciaccess0:arm64 (0.16-0ubuntu1) ... Setting up libkeyutils1:arm64 (1.6-6ubuntu1) ... Setting up libpython3.8-minimal:arm64 (3.8.0-5) ... Setting up mime-support (3.64ubuntu1) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:arm64 (2.63.3-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.7.1ubuntu1) ... Setting up libmagic1:arm64 (1:5.37-6) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.37-6) ... Setting up libaec0:arm64 (1.0.4-1) ... Setting up libicu63:arm64 (63.2-2) ... Setting up python-babel-localedata (2.6.0+dfsg.1-1) ... Setting up libkrb5support0:arm64 (1.17-6) ... Setting up libpython2.7-stdlib:arm64 (2.7.17-1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:arm64 (3.9.0-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.2.9-1) ... Setting up bash-completion (1:2.9-1ubuntu1) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libevent-core-2.1-7:arm64 (2.1.11-stable-1) ... Setting up libevent-2.1-7:arm64 (2.1.11-stable-1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libk5crypto3:arm64 (1.17-6) ... Setting up libltdl7:arm64 (2.4.6-11) ... Setting up libgfortran5:arm64 (9.2.1-21ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1ubuntu3) ... Setting up python3.8-minimal (3.8.0-5) ... Setting up ocl-icd-libopencl1:arm64 (2.2.11-1ubuntu1) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libnl-3-200:arm64 (3.4.0-1) ... Setting up openmpi-common (4.0.2-5) ... Setting up libsub-override-perl (0.09-2) ... Setting up sgml-base (1.29.1) ... Setting up libkrb5-3:arm64 (1.17-6) ... Setting up libmpdec2:arm64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up libpython3.8-stdlib:arm64 (3.8.0-5) ... Setting up python3.8 (3.8.0-5) ... Setting up libbsd0:arm64 (0.10.0-1) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-8ubuntu1) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libsz2:arm64 (1.0.4-1) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up libevent-pthreads-2.1-7:arm64 (2.1.11-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.6.3-1) ... Setting up libpython3.7-stdlib:arm64 (3.7.5-2) ... Setting up liblapack3:arm64 (3.9.0-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up python2.7 (2.7.17-1) ... Setting up libpython3.7:arm64 (3.7.5-2) ... Setting up libtool (2.4.6-11) ... Setting up libpython2-stdlib:arm64 (2.7.17-1) ... Setting up libpython3.7-dev:arm64 (3.7.5-2) ... Setting up libedit2:arm64 (3.1-20191211-1) ... Setting up m4 (1.4.18-4) ... Setting up python2 (2.7.17-1) ... Setting up libnl-route-3-200:arm64 (3.4.0-1) ... Setting up help2man (1.47.12) ... Setting up libpython3.8:arm64 (3.8.0-5) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libhwloc15:arm64 (2.1.0+dfsg-2) ... Setting up libgssapi-krb5-2:arm64 (1.17-6) ... Setting up libcroco3:arm64 (0.6.13-1) ... Setting up libjs-sphinxdoc (1.8.5-4) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3-stdlib:arm64 (3.7.5-1ubuntu1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.3-7) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.5-2) ... Setting up cython (0.29.14-0.1) ... Setting up libibverbs1:arm64 (27.0-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libpython3-dev:arm64 (3.7.5-1ubuntu1) ... Setting up openssh-client (1:8.1p1-1) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up libhwloc-plugins:arm64 (2.1.0+dfsg-2) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-markupsafe (1.1.0-1build1) ... Setting up python3.7-dev (3.7.5-2) ... Setting up python3-tz (2019.3-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-2build1) ... Setting up python3-roman (2.0.0-3build1) ... Setting up python3-decorator (4.3.0-1.1build1) ... Setting up python3-jinja2 (2.10-2ubuntu2) ... Setting up python3-pygments (2.3.1+dfsg-1ubuntu2) ... Setting up python3-pyparsing (2.4.2-1) ... Setting up python3-certifi (2019.11.28-1) ... Setting up libpython3.8-dev:arm64 (3.8.0-5) ... Setting up libpython3-all-dev:arm64 (3.7.5-1ubuntu1) ... Setting up sphinx-common (1.8.5-4) ... Setting up python3-idna (2.6-2build1) ... Setting up cython3 (0.29.14-0.1) ... Setting up python3-urllib3 (1.24.1-1ubuntu2) ... Setting up python3.8-dev (3.8.0-5) ... Setting up python3-dateutil (2.7.3-3) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up python3-imagesize (1.2.0-1) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu1) ... Setting up python3-attr (18.2.0-1build1) ... Setting up python3-setuptools (41.4.0-1) ... Setting up libpmix2:arm64 (3.1.4-1build1) ... Setting up python3-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.3.7-1) ... Setting up python3-alabaster (0.7.8-1build1) ... Setting up po-debconf (1.0.21) ... Setting up libopenmpi3:arm64 (4.0.2-5) ... Setting up python3-all (3.7.5-1ubuntu1) ... Setting up python3-click (7.0-2) ... Setting up python3-nose (1.3.7-4) ... Setting up python3-packaging (19.1-2) ... Setting up libhdf5-openmpi-103:arm64 (1.10.4+repack-10) ... Setting up python3-chardet (3.0.4-4) ... Setting up python3-dev (3.7.5-1ubuntu1) ... Setting up python3-requests (2.21.0-1) ... Setting up python3-numpy (1:1.17.4-3ubuntu2) ... Setting up python3-future (0.16.0-1) ... 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 openmpi-bin (4.0.2-5) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-all-dev (3.7.5-1ubuntu1) ... Setting up python3-scipy (1.3.2-0ubuntu1) ... /usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:495: SyntaxWarning: "is" with a literal. Did you mean "=="? if cons['type'] is 'ineq': /usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:743: SyntaxWarning: "is not" with a literal. Did you mean "!="? if len(self.X_min) is not 0: Setting up python3-pandas-lib (0.25.3+dfsg-4) ... Setting up mpi-default-bin (1.13) ... Setting up python3-mpi4py (3.0.2-13build1) ... Setting up python3-pandas (0.25.3+dfsg-4) ... /usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="? False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632 /usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="? False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632 Setting up python3-h5py (2.10.0-2build1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.7.1ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... Processing triggers for sgml-base (1.29.1) ... Setting up docutils-common (0.15.2+dfsg-1) ... Processing triggers for sgml-base (1.29.1) ... Setting up python3-docutils (0.15.2+dfsg-1) ... 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 (1.8.5-4) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Setting up sbuild-build-depends-python-biom-format-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic arm64 (aarch64) Toolchain package versions: binutils_2.33.1-6ubuntu3 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-21ubuntu1 gcc-9_9.2.1-21ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 linux-libc-dev_5.3.0-24.26 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 bash-completion_1:2.9-1ubuntu1 binutils_2.33.1-6ubuntu3 binutils-aarch64-linux-gnu_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-21ubuntu1 cython_0.29.14-0.1 cython3_0.29.14-0.1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017ubuntu1 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 docutils-common_0.15.2+dfsg-1 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu2 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu4 file_1:5.37-6 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-21ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-21ubuntu1 gcc-9-base_9.2.1-21ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.3-1build1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 help2man_1.47.12 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libaec0_1.0.4-1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.5 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-21ubuntu1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-21ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.33.1-6ubuntu3 libblas3_3.9.0-1 libblkid1_2.34-0.1ubuntu4 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcc1-0_9.2.1-21ubuntu1 libcom-err2_1.45.3-4ubuntu2 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu2 libdebhelper-perl_12.7.1ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdpkg-perl_1.19.7ubuntu2 libedit2_3.1-20191211-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.11-stable-1 libevent-core-2.1-7_2.1.11-stable-1 libevent-pthreads-2.1-7_2.1.11-stable-1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.3-4ubuntu2 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu4 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-21ubuntu1 libgcc1_1:9.2.1-21ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-21ubuntu1 libglib2.0-0_2.63.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-21ubuntu1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libhdf5-openmpi-103_1.10.4+repack-10 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhwloc-plugins_2.1.0+dfsg-2 libhwloc15_2.1.0+dfsg-2 libibverbs1_27.0-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_9.2.1-21ubuntu1 libjs-jquery_3.3.1~dfsg-3 libjs-sphinxdoc_1.8.5-4 libjs-underscore_1.9.1~dfsg-1 libjson-c4_0.13.1+dfsg-6 libk5crypto3_1.17-6 libkeyutils1_1.6-6ubuntu1 libkmod2_26-3ubuntu1 libkrb5-3_1.17-6 libkrb5support0_1.17-6 liblapack3_3.9.0-1 liblbfgsb0_3.0+dfsg.3-7 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_9.2.1-21ubuntu1 libltdl7_2.4.6-11 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1ubuntu4 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnl-3-200_3.4.0-1 libnl-route-3-200_3.4.0-1 libnpth0_1.6-1 libopenmpi3_4.0.2-5 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpciaccess0_0.16-0ubuntu1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpmix2_3.1.4-1build1 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpython2-stdlib_2.7.17-1 libpython2.7-minimal_2.7.17-1 libpython2.7-stdlib_2.7.17-1 libpython3-all-dev_3.7.5-1ubuntu1 libpython3-dev_3.7.5-1ubuntu1 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7_3.7.5-2 libpython3.7-dev_3.7.5-2 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libpython3.8_3.8.0-5 libpython3.8-dev_3.8.0-5 libpython3.8-minimal_3.8.0-5 libpython3.8-stdlib_3.8.0-5 libreadline8_8.0-3 libseccomp2_2.4.2-2ubuntu1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu4 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu2 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244-3ubuntu1 libsz2_1.0.4-1 libtasn1-6_4.15.0-2 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-11 libtsan0_9.2.1-21ubuntu1 libubsan1_9.2.1-21ubuntu1 libuchardet0_0.0.6-3 libudev1_244-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu4 libxml2_2.9.4+dfsg1-8ubuntu1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.0-24.26 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu4 mpi-default-bin_1.13 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 ocl-icd-libopencl1_2.2.11-1ubuntu1 openmpi-bin_4.0.2-5 openmpi-common_4.0.2-5 openssh-client_1:8.1p1-1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python-babel-localedata_2.6.0+dfsg.1-1 python2_2.7.17-1 python2-minimal_2.7.17-1 python2.7_2.7.17-1 python2.7-minimal_2.7.17-1 python3_3.7.5-1ubuntu1 python3-alabaster_0.7.8-1build1 python3-all_3.7.5-1ubuntu1 python3-all-dev_3.7.5-1ubuntu1 python3-attr_18.2.0-1build1 python3-babel_2.6.0+dfsg.1-1 python3-certifi_2019.11.28-1 python3-chardet_3.0.4-4 python3-click_7.0-2 python3-colorama_0.3.7-1 python3-dateutil_2.7.3-3 python3-decorator_4.3.0-1.1build1 python3-dev_3.7.5-1ubuntu1 python3-distutils_3.8.0-1 python3-docutils_0.15.2+dfsg-1 python3-future_0.16.0-1 python3-h5py_2.10.0-2build1 python3-idna_2.6-2build1 python3-imagesize_1.2.0-1 python3-jinja2_2.10-2ubuntu2 python3-lib2to3_3.8.0-1 python3-markupsafe_1.1.0-1build1 python3-minimal_3.7.5-1ubuntu1 python3-mpi4py_3.0.2-13build1 python3-nose_1.3.7-4 python3-numpy_1:1.17.4-3ubuntu2 python3-packaging_19.1-2 python3-pandas_0.25.3+dfsg-4 python3-pandas-lib_0.25.3+dfsg-4 python3-pkg-resources_41.4.0-1 python3-pygments_2.3.1+dfsg-1ubuntu2 python3-pyparsing_2.4.2-1 python3-requests_2.21.0-1 python3-roman_2.0.0-3build1 python3-scipy_1.3.2-0ubuntu1 python3-setuptools_41.4.0-1 python3-six_1.12.0-2build1 python3-sphinx_1.8.5-4 python3-tz_2019.3-1 python3-urllib3_1.24.1-1ubuntu2 python3.7_3.7.5-2 python3.7-dev_3.7.5-2 python3.7-minimal_3.7.5-2 python3.8_3.8.0-5 python3.8-dev_3.8.0-5 python3.8-minimal_3.8.0-5 readline-common_8.0-3 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_1.29.1 sphinx-common_1.8.5-4 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu4 xml-core_0.18+nmu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Aug 16 03:07:47 2019 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-biom-format_2.1.7+dfsg-3ubuntu2.dsc dpkg-source: info: extracting python-biom-format in python-biom-format-2.1.7+dfsg dpkg-source: info: unpacking python-biom-format_2.1.7+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biom-format_2.1.7+dfsg-3ubuntu2.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 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18342686 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18342686 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18342686 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-biom-format dpkg-buildpackage: info: source version 2.1.7+dfsg-3ubuntu2 dpkg-buildpackage: info: source distribution eoan dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3,bash-completion,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean --test-nose -i python{version} -p "3.8 3.7" I: pybuild base:217: python3.8 setup.py clean running clean removing '/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.7' 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 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 build-arch dh build-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 pybuild --configure --test-nose -i python{version} -p "3.8 3.7" I: pybuild base:217: python3.8 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/python-biom-format-2.1.7+dfsg' # arch USE_CYTHON=true dh_auto_build pybuild --build --test-nose -i python{version} -p "3.8 3.7" I: pybuild base:217: /usr/bin/python3.8 setup.py build 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 build running build_py creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/err.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/parse.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/util.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/exception.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_summarizer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_converter.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/uc_processor.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_subsetter.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/metadata_adder.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_normalizer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/installation_informer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_head.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/util.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_ids.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli copying biom/cli/table_validator.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests copying biom/tests/test_err.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests copying biom/tests/test_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests copying biom/tests/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests copying biom/tests/test_util.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests copying biom/tests/test_parse.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests copying biom/tests/long_lines.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli 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' /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: /<>/python-biom-format-2.1.7+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: /<>/python-biom-format-2.1.7+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: /<>/python-biom-format-2.1.7+dfsg/biom/_transform.pyx tree = Parsing.p_module(s, pxd, full_module_name) 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 -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/_filter.pyx -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/_subsample.c -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/_subsample.pyx -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/_transform.c -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom copying biom/_transform.pyx -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/assets copying biom/assets/exercise_api.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/assets copying biom/assets/exercise_cli.sh -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/assets creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables copying biom/tests/test_data/bad_table.txt -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/empty.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data creating /<>/python-biom-format-2.1.7+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 -> /<>/python-biom-format-2.1.7+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 -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data running build_ext building 'biom._filter' extension creating build creating build/temp.linux-arm64-3.8 creating build/temp.linux-arm64-3.8/biom aarch64-linux-gnu-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=/<>/python-biom-format-2.1.7+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-arm64-3.8/biom/_filter.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830, 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:617: /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 " \ | ^~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/biom/_filter.o -o /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/_filter.cpython-38-aarch64-linux-gnu.so building 'biom._transform' extension aarch64-linux-gnu-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=/<>/python-biom-format-2.1.7+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-arm64-3.8/biom/_transform.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830, 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:617: /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 " \ | ^~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/biom/_transform.o -o /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/_transform.cpython-38-aarch64-linux-gnu.so building 'biom._subsample' extension aarch64-linux-gnu-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=/<>/python-biom-format-2.1.7+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-arm64-3.8/biom/_subsample.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830, 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:617: /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 " \ | ^~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/biom/_subsample.o -o /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/_subsample.cpython-38-aarch64-linux-gnu.so I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/err.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/parse.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/util.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/exception.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_summarizer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_converter.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/uc_processor.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_subsetter.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/metadata_adder.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_normalizer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/installation_informer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_head.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/util.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_ids.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli copying biom/cli/table_validator.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/cli creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests copying biom/tests/test_err.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests copying biom/tests/test_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests copying biom/tests/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests copying biom/tests/test_util.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests copying biom/tests/test_parse.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests copying biom/tests/long_lines.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli running 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 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 -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/_filter.pyx -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/_subsample.c -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/_subsample.pyx -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/_transform.c -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom copying biom/_transform.pyx -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/assets copying biom/assets/exercise_api.py -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/assets copying biom/assets/exercise_cli.sh -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/assets creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables copying biom/tests/test_data/bad_table.txt -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/empty.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data creating /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data running build_ext building 'biom._filter' extension creating build/temp.linux-arm64-3.7 creating build/temp.linux-arm64-3.7/biom aarch64-linux-gnu-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=/<>/python-biom-format-2.1.7+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/python3.7m -c biom/_filter.c -o build/temp.linux-arm64-3.7/biom/_filter.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830, 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:617: /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 " \ | ^~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/biom/_filter.o -o /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/_filter.cpython-37m-aarch64-linux-gnu.so building 'biom._transform' extension aarch64-linux-gnu-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=/<>/python-biom-format-2.1.7+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/python3.7m -c biom/_transform.c -o build/temp.linux-arm64-3.7/biom/_transform.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830, 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:617: /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 " \ | ^~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/biom/_transform.o -o /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/_transform.cpython-37m-aarch64-linux-gnu.so building 'biom._subsample' extension aarch64-linux-gnu-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=/<>/python-biom-format-2.1.7+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/python3.7m -c biom/_subsample.c -o build/temp.linux-arm64-3.7/biom/_subsample.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830, 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:617: /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 " \ | ^~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/biom/_subsample.o -o /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/_subsample.cpython-37m-aarch64-linux-gnu.so # indep: PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html Running Sphinx v1.8.5 making output directory... [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.table': no module named biom.table Failed to import 'biom': no module named biom 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: 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 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 /<>/python-biom-format-2.1.7+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 /<>/python-biom-format-2.1.7+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 /<>/python-biom-format-2.1.7+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 /<>/python-biom-format-2.1.7+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... writing additional pages... search 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 v1.8.5 making output directory... [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.table': no module named biom.table Failed to import 'biom': no module named biom building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: 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 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 } build succeeded, 2 warnings. The manual pages are in build/man. make[1]: Leaving directory '/<>/python-biom-format-2.1.7+dfsg' rm -f debian/python3-biom-format.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-biom-format-2.1.7+dfsg' cp -a examples /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython2_2.7_biom-format/build cp -a examples /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build dh_auto_test pybuild --test --test-nose -i python{version} -p "3.8 3.7" I: pybuild base:217: cd /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build; python3.8 -m nose -v /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3255: SyntaxWarning: "is" with a literal. Did you mean "=="? if axis is 'both' and not (alignable_o and alignable_s): /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3257: SyntaxWarning: "is" with a literal. Did you mean "=="? elif axis is 'sample' and not alignable_s: /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3259: SyntaxWarning: "is" with a literal. Did you mean "=="? elif axis is 'observation' and not alignable_o: /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3261: SyntaxWarning: "is" with a literal. Did you mean "=="? elif axis is 'detect' and not (alignable_o or alignable_s): /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3264: SyntaxWarning: "is" with a literal. Did you mean "=="? if axis is 'both': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3266: SyntaxWarning: "is" with a literal. Did you mean "=="? elif axis is 'detect': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3272: SyntaxWarning: "is" with a literal. Did you mean "=="? elif axis is 'sample': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3274: SyntaxWarning: "is" with a literal. Did you mean "=="? elif axis is 'observation': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3509: SyntaxWarning: "is" with a literal. Did you mean "=="? if sample is 'union': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3511: SyntaxWarning: "is" with a literal. Did you mean "=="? elif sample is 'intersection': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3517: SyntaxWarning: "is" with a literal. Did you mean "=="? if observation is 'union': /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:3520: SyntaxWarning: "is" with a literal. Did you mean "=="? elif observation is 'intersection': 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 ... /<>/python-biom-format-2.1.7+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] /<>/python-biom-format-2.1.7+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 ... ERROR 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 ... ERROR 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) ... ERROR 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_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 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 ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_parse.py:237: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. Table.from_hdf5(h5py.File('test_data/test.biom')) ok test the biom table parser subsetting ... ok tests for parse_biom_table when we have h5py ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_parse.py:276: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = parse_biom_table(h5py.File('test_data/test.biom')) 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_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 ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:629: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom')) ok test_from_hdf5_custom_parsers (biom.tests.test_table.TableTests) ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:610: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom'), ok Parse a hdf5 formatted BIOM table w/o metadata ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:595: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/empty.biom')) ok HDF5 biom parse successfully loads an empty table ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:914: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/empty.biom')) ok test_from_hdf5_issue_731 (biom.tests.test_table.TableTests) ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:619: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom')) 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 ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:835: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom'), /<>/python-biom-format-2.1.7+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] /<>/python-biom-format-2.1.7+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 ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:807: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom'), ok Parse a sample subset of a hdf5 formatted BIOM table ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:743: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom'), ids=samples) ok Parse a sample subset of a hdf5 formatted BIOM table ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:715: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. t = Table.from_hdf5(h5py.File('test_data/test.biom'), ids=samples, ok hdf5 biom table parse throws error with invalid parameters ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:898: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. Table.from_hdf5(h5py.File('test_data/test.biom'), /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:903: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details. Table.from_hdf5(h5py.File('test_data/test.biom'), 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) ... /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py:1476: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead. See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more. exp = pd.SparseDataFrame(np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]]), /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:4048: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead. >>> series = pd.Series(pd.SparseArray(...)) See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more. mat = [pd.SparseSeries(r.toarray().squeeze()) /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py:4052: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead. See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more. return constructor(mat, index=index, columns=columns) /usr/lib/python3/dist-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead. >>> series = pd.Series(pd.SparseArray(...)) See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more. return klass(values, index=self.index, name=items, fastpath=True) ok test_to_dataframe_dense (biom.tests.test_table.TableTests) ... ok 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 an invalid HDF5 table ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py", line 155, in skipper_func return f(*args, **kwargs) File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py", line 88, in test_invalid_hdf5 copy(self.hdf5_file_valid, 'invalid.hdf5') File "/usr/lib/python3.8/shutil.py", line 409, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/usr/lib/python3.8/shutil.py", line 259, in copyfile with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst: FileNotFoundError: [Errno 2] No such file or directory: '/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom' ====================================================================== ERROR: Test a valid HDF5 table ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py", line 155, in skipper_func return f(*args, **kwargs) File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py", line 79, in test_valid_hdf5 obs = self.cmd(table=self.hdf5_file_valid) File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", line 112, in __call__ return self.run(table=table, format_version=format_version, File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", line 78, in run is_json = not is_hdf5_file(kwargs['table']) File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/util.py", line 518, in is_hdf5_file with open(fp, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom' ====================================================================== ERROR: test_valid_hdf5_metadata_v210 (biom.tests.test_cli.test_validate_table.TableValidatorTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py", line 155, in skipper_func return f(*args, **kwargs) File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py", line 62, in test_valid_hdf5_metadata_v210 obs = self.cmd(table=self.hdf5_file_valid, File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", line 112, in __call__ return self.run(table=table, format_version=format_version, File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", line 78, in run is_json = not is_hdf5_file(kwargs['table']) File "/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/util.py", line 518, in is_hdf5_file with open(fp, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom' ---------------------------------------------------------------------- Ran 336 tests in 17.930s FAILED (SKIP=1, errors=3) E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /<>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build; python3.8 -m nose -v dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.8 3.7" returned exit code 13 make[1]: *** [debian/rules:36: override_dh_auto_test] Error 255 make[1]: Leaving directory '/<>/python-biom-format-2.1.7+dfsg' make: *** [debian/rules:18: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200105-1303 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 168764 Build-Time: 99 Distribution: focal Fail-Stage: build Host Architecture: arm64 Install-Time: 165 Job: python-biom-format_2.1.7+dfsg-3ubuntu2.dsc Machine Architecture: arm64 Package: python-biom-format Package-Time: 268 Source-Version: 2.1.7+dfsg-3ubuntu2 Space: 168764 Status: attempted Version: 2.1.7+dfsg-3ubuntu2 -------------------------------------------------------------------------------- Finished at 20200105-1303 Build needed 00:04:28, 168764k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18342686 Scanning for processes to kill in build PACKAGEBUILD-18342686