https://launchpad.net/ubuntu/+source/python-skbio/0.5.6-6build1/+build/23248678 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-033 5.4.0-104-generic #118-Ubuntu SMP Wed Mar 2 19:03:41 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_209~536~ubuntu20.04.1 python3-lpbuildd_209~536~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 17 Mar 10:38:56 ntpdate[1751]: adjust time server 10.211.37.1 offset 0.003342 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-23248678 --image-type chroot /home/buildd/filecache-default/c698bf6badd89264039f6cdfcd7c983f87611a3e Creating target for build PACKAGEBUILD-23248678 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-23248678 Starting target for build PACKAGEBUILD-23248678 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-23248678 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23248678 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-23248678 Updating target for build PACKAGEBUILD-23248678 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf Packages [1347 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe armhf Packages [13.1 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5644 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf Packages [73.6 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [30.6 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf Packages [352 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [176 kB] Fetched 21.8 MB in 8s (2897 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: libperl5.32 libssl1.1 perl-modules-5.32 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: gcc-12-base libperl5.34 libsemanage2 libsepol2 libssl3 perl-modules-5.34 The following packages will be upgraded: apt base-files bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 ca-certificates coreutils cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libffi8 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libprocps8 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libunistring2 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata usrmerge util-linux zlib1g 132 upgraded, 6 newly installed, 1 to remove and 0 not upgraded. Need to get 86.2 MB of archives. After this operation, 298 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt-dev armhf 1:4.4.27-1 [122 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf libc6-dev armhf 2.35-0ubuntu3 [1331 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libc-dev-bin armhf 2.35-0ubuntu3 [19.0 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf libaudit-common all 1:3.0.7-1 [4782 B] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf libcap-ng0 armhf 0.7.9-2.2build3 [10.1 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf libaudit1 armhf 1:3.0.7-1 [43.7 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf libc6 armhf 2.35-0ubuntu3 [2517 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf libc-bin armhf 2.35-0ubuntu3 [546 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf perl-modules-5.34 all 5.34.0-3ubuntu1 [2975 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf libperl5.34 armhf 5.34.0-3ubuntu1 [4039 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main armhf perl armhf 5.34.0-3ubuntu1 [232 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf perl-base armhf 5.34.0-3ubuntu1 [1613 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf bzip2 armhf 1.0.8-5 [34.2 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf libbz2-1.0 armhf 1.0.8-5 [31.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libgdbm6 armhf 1.23-1 [30.0 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf libgdbm-compat4 armhf 1.23-1 [6070 B] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf zlib1g armhf 1:1.2.11.dfsg-2ubuntu8 [51.3 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf debconf all 1.5.79ubuntu1 [126 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf libpam0g armhf 1.4.0-11ubuntu1 [55.6 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt1 armhf 1:4.4.27-1 [94.0 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf linux-libc-dev armhf 5.15.0-23.23 [1286 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-12-base armhf 12-20220313-1ubuntu1 [18.9 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-s1 armhf 12-20220313-1ubuntu1 [42.5 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf base-files armhf 12ubuntu2 [63.0 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf debianutils armhf 5.5-1ubuntu1 [106 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf bash armhf 5.1-6ubuntu1 [655 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf bsdutils armhf 1:2.37.2-4ubuntu3 [87.0 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf coreutils armhf 8.32-4.1ubuntu1 [1301 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf libgpg-error0 armhf 1.43-3 [61.9 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf libgcrypt20 armhf 1.9.4-3ubuntu2 [438 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++6 armhf 12-20220313-1ubuntu1 [617 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf libssl3 armhf 3.0.1-0ubuntu1 [1577 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf libargon2-1 armhf 0~20171227-0.3 [21.0 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf libblkid1 armhf 2.37.2-4ubuntu3 [136 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf libpcre2-8-0 armhf 10.39-3 [190 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main armhf libselinux1 armhf 3.3-1build1 [66.7 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main armhf libudev1 armhf 249.11-0ubuntu1 [69.8 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main armhf libdevmapper1.02.1 armhf 2:1.02.175-2.1ubuntu4 [134 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main armhf libuuid1 armhf 2.37.2-4ubuntu3 [23.6 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main armhf libcryptsetup12 armhf 2:2.4.3-1ubuntu1 [189 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main armhf libgmp10 armhf 2:6.2.1+dfsg-3ubuntu1 [205 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf libunistring2 armhf 1.0-1 [533 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main armhf libidn2-0 armhf 2.3.2-2 [67.8 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main armhf libffi8 armhf 3.4.2-4 [19.0 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf libp11-kit0 armhf 0.24.0-6 [219 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf libtasn1-6 armhf 4.18.0-4 [36.3 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf libgnutls30 armhf 3.7.3-4ubuntu1 [934 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf systemd-sysv armhf 249.11-0ubuntu1 [10.5 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main armhf systemd-timesyncd armhf 249.11-0ubuntu1 [31.0 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf libacl1 armhf 2.3.1-1 [14.9 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libapparmor1 armhf 3.0.4-2ubuntu2 [33.0 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf libip4tc2 armhf 1.8.7-1ubuntu4 [17.7 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf libzstd1 armhf 1.4.8+dfsg-3 [285 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf libkmod2 armhf 29-1ubuntu1 [40.9 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main armhf libmount1 armhf 2.37.2-4ubuntu3 [152 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main armhf libseccomp2 armhf 2.5.3-2ubuntu1 [46.8 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main armhf login armhf 1:4.8.1-2ubuntu2 [186 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf util-linux armhf 2.37.2-4ubuntu3 [1130 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf mount armhf 2.37.2-4ubuntu3 [125 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf systemd armhf 249.11-0ubuntu1 [4453 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf libsystemd0 armhf 249.11-0ubuntu1 [295 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf libxxhash0 armhf 0.8.1-1 [26.3 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libapt-pkg6.0 armhf 2.4.1 [899 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf dpkg armhf 1.21.1ubuntu1 [1204 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-3 [83.8 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main armhf grep armhf 3.7-1 [150 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses6 armhf 6.3-2 [87.5 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf libncursesw6 armhf 6.3-2 [117 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf libtinfo6 armhf 6.3-2 [87.9 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-bin armhf 6.3-2 [175 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main armhf sed armhf 4.8-1ubuntu1 [186 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main armhf init-system-helpers all 1.62 [38.5 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-base all 6.3-2 [20.1 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main armhf sysvinit-utils armhf 3.01-1ubuntu1 [20.5 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf gpgv armhf 2.2.27-3ubuntu1 [186 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf apt armhf 2.4.1 [1367 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf libsepol2 armhf 3.3-1 [263 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main armhf libsemanage-common all 3.3-1build1 [10.0 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main armhf libsemanage2 armhf 3.3-1build1 [84.1 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main armhf passwd armhf 1:4.8.1-2ubuntu2 [740 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules-bin armhf 1.4.0-11ubuntu1 [35.5 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules armhf 1.4.0-11ubuntu1 [263 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main armhf logsave armhf 1.46.5-2ubuntu1 [10.1 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf libext2fs2 armhf 1.46.5-2ubuntu1 [191 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main armhf e2fsprogs armhf 1.46.5-2ubuntu1 [566 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main armhf init armhf 1.62 [5412 B] Get:87 http://ftpmaster.internal/ubuntu jammy/main armhf libattr1 armhf 1:2.5.1-1 [12.2 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main armhf libcom-err2 armhf 1.46.5-2ubuntu1 [9002 B] Get:89 http://ftpmaster.internal/ubuntu jammy/main armhf libdebconfclient0 armhf 0.261ubuntu1 [6552 B] Get:90 http://ftpmaster.internal/ubuntu jammy/main armhf libk5crypto3 armhf 1.19.2-2 [83.6 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main armhf libkrb5support0 armhf 1.19.2-2 [30.4 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main armhf libkrb5-3 armhf 1.19.2-2 [330 kB] Get:93 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jammy-proposed/main armhf binutils armhf 2.38-3ubuntu1 [3162 B] Get:113 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf binutils-common armhf 2.38-3ubuntu1 [221 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main armhf cpp-11 armhf 11.2.0-18ubuntu1 [7842 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11-base armhf 11.2.0-18ubuntu1 [21.0 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main armhf libprocps8 armhf 2:3.3.17-6ubuntu2 [32.7 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main armhf libss2 armhf 1.46.5-2ubuntu1 [10.1 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/main armhf mawk armhf 1.3.4.20200120-3 [91.5 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/main armhf procps armhf 2:3.3.17-6ubuntu2 [372 kB] Get:120 http://ftpmaster.internal/ubuntu jammy/main armhf sensible-utils all 0.0.17 [20.1 kB] Get:121 http://ftpmaster.internal/ubuntu jammy/main armhf usrmerge all 25ubuntu2 [54.7 kB] Get:122 http://ftpmaster.internal/ubuntu jammy/main armhf openssl armhf 3.0.1-0ubuntu1 [1150 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main armhf ca-certificates all 20211016 [148 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/main armhf readline-common all 8.1.2-1 [53.5 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/main armhf libreadline8 armhf 8.1.2-1 [128 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main armhf libsqlite3-0 armhf 3.37.2-2 [549 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/main armhf tzdata all 2021e-1ubuntu1 [343 kB] Get:128 http://ftpmaster.internal/ubuntu jammy/main armhf dpkg-dev all 1.21.1ubuntu1 [922 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/main armhf libdpkg-perl all 1.21.1ubuntu1 [236 kB] Get:130 http://ftpmaster.internal/ubuntu jammy/main armhf make armhf 4.3-4.1build1 [163 kB] Get:131 http://ftpmaster.internal/ubuntu jammy/main armhf lto-disabled-list all 23 [12.5 kB] Get:132 http://ftpmaster.internal/ubuntu jammy/main armhf libfakeroot armhf 1.28-1ubuntu1 [26.3 kB] Get:133 http://ftpmaster.internal/ubuntu jammy/main armhf fakeroot armhf 1.28-1ubuntu1 [62.2 kB] Get:134 http://ftpmaster.internal/ubuntu jammy/main armhf gpg armhf 2.2.27-3ubuntu1 [483 kB] Get:135 http://ftpmaster.internal/ubuntu jammy/main armhf gpgconf armhf 2.2.27-3ubuntu1 [115 kB] Get:136 http://ftpmaster.internal/ubuntu jammy/main armhf gpg-agent armhf 2.2.27-3ubuntu1 [227 kB] Get:137 http://ftpmaster.internal/ubuntu jammy/main armhf lockfile-progs armhf 0.1.19 [9508 B] Get:138 http://ftpmaster.internal/ubuntu jammy/main armhf pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 86.2 MB in 4s (22.2 MB/s) (Reading database ... 12985 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.27-1_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libc6-dev_2.35-0ubuntu3_armhf.deb ... Unpacking libc6-dev:armhf (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.35-0ubuntu3_armhf.deb ... Unpacking libc-dev-bin (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Preparing to unpack .../libaudit-common_1%3a3.0.7-1_all.deb ... Unpacking libaudit-common (1:3.0.7-1) over (1:3.0-2ubuntu3) ... Setting up libaudit-common (1:3.0.7-1) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.9-2.2build3_armhf.deb ... Unpacking libcap-ng0:armhf (0.7.9-2.2build3) over (0.7.9-2.2build2) ... Setting up libcap-ng0:armhf (0.7.9-2.2build3) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.7-1_armhf.deb ... 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Setting up lto-disabled-list (23) ... Setting up init (1.62) ... Setting up libsqlite3-0:armhf (3.37.2-2) ... Setting up binutils-common:armhf (2.38-3ubuntu1) ... Setting up linux-libc-dev:armhf (5.15.0-23.23) ... Setting up libctf-nobfd0:armhf (2.38-3ubuntu1) ... Setting up libgomp1:armhf (12-20220313-1ubuntu1) ... Setting up perl-modules-5.34 (5.34.0-3ubuntu1) ... Setting up bzip2 (1.0.8-5) ... Setting up libfakeroot:armhf (1.28-1ubuntu1) ... Setting up libasan6:armhf (11.2.0-18ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 17 10:40:04 UTC 2022. Universal Time is now: Thu Mar 17 10:40:04 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.28-1ubuntu1) ... Setting up make (4.3-4.1build1) ... Setting up libncurses6:armhf (6.3-2) ... Setting up libmpc3:armhf (1.2.1-1) ... Setting up systemd-timesyncd (249.11-0ubuntu1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:armhf (12-20220313-1ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:armhf (1.46.5-2ubuntu1) ... Setting up libncursesw6:armhf (6.3-2) ... Setting up logsave (1.46.5-2ubuntu1) ... Setting up libubsan1:armhf (12-20220313-1ubuntu1) ... Setting up libgcc-11-dev:armhf (11.2.0-18ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:armhf (1:4.4.27-1) ... Setting up mawk (1.3.4.20200120-3) ... Setting up libbinutils:armhf (2.38-3ubuntu1) ... Setting up libisl23:armhf (0.24-2) ... Setting up libc-dev-bin (2.35-0ubuntu3) ... Setting up openssl (3.0.1-0ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.1.2-1) ... Setting up libcc1-0:armhf (12-20220313-1ubuntu1) ... Setting up libprocps8:armhf (2:3.3.17-6ubuntu2) ... Setting up libgdbm6:armhf (1.23-1) ... Setting up libctf0:armhf (2.38-3ubuntu1) ... Setting up cpp-11 (11.2.0-18ubuntu1) ... Setting up pkgbinarymangler (149) ... Setting up libreadline8:armhf (8.1.2-1) ... Setting up e2fsprogs (1.46.5-2ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up libgdbm-compat4:armhf (1.23-1) ... Setting up procps (2:3.3.17-6ubuntu2) ... Installing new version of config file /etc/init.d/procps ... Installing new version of config file /etc/sysctl.d/README.sysctl ... Setting up gpgconf (2.2.27-3ubuntu1) ... Setting up libc6-dev:armhf (2.35-0ubuntu3) ... Setting up binutils-arm-linux-gnueabihf (2.38-3ubuntu1) ... Setting up gpg (2.2.27-3ubuntu1) ... Setting up libperl5.34:armhf (5.34.0-3ubuntu1) ... Setting up gpg-agent (2.2.27-3ubuntu1) ... Setting up binutils (2.38-3ubuntu1) ... Setting up perl (5.34.0-3ubuntu1) ... Setting up libdpkg-perl (1.21.1ubuntu1) ... Setting up libstdc++-11-dev:armhf (11.2.0-18ubuntu1) ... Setting up gcc-11 (11.2.0-18ubuntu1) ... Setting up g++-11 (11.2.0-18ubuntu1) ... Setting up dpkg-dev (1.21.1ubuntu1) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23248678 armhf jammy-proposed -c chroot:build-PACKAGEBUILD-23248678 --arch=armhf --dist=jammy-proposed --nolog python-skbio_0.5.6-6build1.dsc Initiating build PACKAGEBUILD-23248678 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-104-generic #118-Ubuntu SMP Wed Mar 2 19:03:41 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-033.buildd +==============================================================================+ | python-skbio 0.5.6-6build1 (armhf) Thu, 17 Mar 2022 10:40:16 +0000 | +==============================================================================+ Package: python-skbio Version: 0.5.6-6build1 Source Version: 0.5.6-6build1 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23248678/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-skbio-ORJLmZ/resolver-ehABrd' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-skbio_0.5.6-6build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-skbio-ORJLmZ/python-skbio-0.5.6' with '<>' I: NOTICE: Log filtering will replace 'build/python-skbio-ORJLmZ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cython3, dh-python, python3-all-dev, python3-setuptools, python3-numpy (>= 1:1.9.2), python3-matplotlib, python3-cachecontrol, python3-decorator, python3-pandas (>= 0.19.2), python3-scipy (>= 1.3.3), python3-ipython, python3-hdmedians (>= 0.14.1), python3-sklearn, python3-natsort, libssw-dev, sphinx-common, libsimde-dev, build-essential, fakeroot, python3-lockfile, python3-pytest Filtered Build-Depends: debhelper-compat (= 13), cython3, dh-python, python3-all-dev, python3-setuptools, python3-numpy (>= 1:1.9.2), python3-matplotlib, python3-cachecontrol, python3-decorator, python3-pandas (>= 0.19.2), python3-scipy (>= 1.3.3), python3-ipython, python3-hdmedians (>= 0.14.1), python3-sklearn, python3-natsort, libssw-dev, sphinx-common, libsimde-dev, build-essential, fakeroot, python3-lockfile, python3-pytest dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [534 B] Get:5 copy:/<>/apt_archive ./ Packages [605 B] Fetched 2102 B in 0s (58.4 kB/s) Reading package lists... Reading package lists... Install main 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: libperl5.32 libssl1.1 perl-modules-5.32 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-lyx gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu70 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenjp2-7 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 libsigsegv2 libsimde-dev libssw-dev libssw0 libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 m4 man-db media-types po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-backcall python3-brotli python3-cachecontrol python3-certifi python3-chardet python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-hdmedians python3-idna python3-importlib-metadata python3-iniconfig python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lib2to3 python3-lockfile python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-more-itertools python3-mpmath python3-msgpack python3-natsort python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-prompt-toolkit python3-ptyprocess python3-py python3-pygments python3-pyparsing python3-pytest python3-requests python3-scipy python3-setuptools python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-toml python3-traitlets python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wcwidth python3-zipp python3.10 python3.10-dev python3.10-minimal sphinx-common tk8.6-blt2.5 ucf unicode-data x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo cython-doc dh-make flit python3-build python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-venv python-attr-doc python-cycler-doc python-ipython-doc python-lockfile-doc python-lxml-doc dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gfortran python-numpy-doc python-pandas-doc python3-statsmodels python-pexpect-doc python-pil-doc subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.10-venv python3.10-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev libmail-sendmail-perl python3-simplejson python3-psutil python3-bs4 python3-html5lib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-tables python3-jinja2 python3-olefile python3-nose python3-sphinx The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-lyx gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu70 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenjp2-7 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 libsigsegv2 libsimde-dev libssw-dev libssw0 libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 m4 man-db media-types po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-backcall python3-brotli python3-cachecontrol python3-certifi python3-chardet python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-hdmedians python3-idna python3-importlib-metadata python3-iniconfig python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lib2to3 python3-lockfile python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-more-itertools python3-mpmath python3-msgpack python3-natsort python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-prompt-toolkit python3-ptyprocess python3-py python3-pygments python3-pyparsing python3-pytest python3-requests python3-scipy python3-setuptools python3-six python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk python3-toml python3-traitlets python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wcwidth python3-zipp python3.10 python3.10-dev python3.10-minimal sbuild-build-depends-main-dummy sphinx-common tk8.6-blt2.5 ucf unicode-data x11-common zlib1g-dev 0 upgraded, 175 newly installed, 0 to remove and 0 not upgraded. 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Setting up bsdextrautils (2.37.2-4ubuntu3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libmagic-mgc (1:5.41-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.71.3-1) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.6ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build4) ... Setting up x11-common (1:7.7+23ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:armhf (1:5.41-2) ... Setting up libdeflate0:armhf (1.10-1ubuntu1) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libqhull-r8.0:armhf (2020.2-4) ... Setting up file (1:5.41-2) ... Setting up libjbig0:armhf (2.1-3.1build2) ... Setting up unicode-data (14.0.0-1.1) ... Setting up autotools-dev (20220109.1) ... 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Setting up liblapack3:armhf (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.14-3ubuntu2) ... Setting up libssw-dev:armhf (1.1-13) ... Setting up libtool (2.4.6-15build1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu4) ... Setting up libwebpdemux2:armhf (1.2.2-2) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libpython3.10-stdlib:armhf (3.10.3-1) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libraqm0:armhf (0.7.0-4ubuntu1) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-8) ... Setting up debugedit (1:5.0-4) ... Setting up libx11-6:armhf (2:1.7.2-2) ... Setting up libtiff5:armhf (4.3.0-6) ... Setting up libfontconfig1:armhf (2.13.1-4.2ubuntu4) ... Setting up libxml2:armhf (2.9.13+dfsg-1) ... Setting up libpython3-stdlib:armhf (3.10.1-0ubuntu2) ... Setting up liblbfgsb0:armhf (3.0+dfsg.3-10) ... Setting up automake (1:1.16.5-1.1ubuntu4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:armhf (3.10.3-1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up python3.10 (3.10.3-1) ... Setting up libxrender1:armhf (1:0.9.10-1build3) ... Setting up libxext6:armhf (2:1.3.4-1) ... Setting up python3 (3.10.1-0ubuntu2) ... Setting up man-db (2.10.1-1) ... 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-tz (2021.3-1) ... Setting up python3-natsort (8.0.2-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.16.0-3) ... 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Setting up libtk8.6:armhf (8.6.12-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-all (3.10.1-0ubuntu2) ... Setting up debhelper (13.6ubuntu1) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-matplotlib-inline (0.1.3-1) ... Setting up python3-fs (2.4.12-1) ... Setting up python3-pygments (2.11.2+dfsg-2) ... Setting up python3-packaging (21.3-1) ... Setting up python3-chardet (4.0.0-1) ... Setting up libpython3-all-dev:armhf (3.10.1-0ubuntu2) ... Setting up python3-pexpect (4.8.0-2ubuntu1) ... Setting up python3-dev (3.10.1-0ubuntu2) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-numpy (1:1.21.5-1build1) ... Setting up python3-hdmedians (0.14.2-4build1) ... Setting up python3-lxml:armhf (4.8.0-1build1) ... Setting up python3-cachecontrol (0.12.10-1) ... Setting up python3-all-dev (3.10.1-0ubuntu2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build1) ... Setting up python3-scipy (1.8.0-1exp2build1) ... Setting up python3-importlib-metadata (4.6.4-1) ... Setting up python3-jedi (0.18.0-1) ... Setting up blt (2.5.3+dfsg-4.1build1) ... Setting up python3-pandas-lib:armhf (1.3.5+dfsg-3) ... Setting up python3-sklearn-lib:armhf (0.23.2-5ubuntu4) ... Setting up python3-tk:armhf (3.10.3-0ubuntu2) ... Setting up python3-pandas (1.3.5+dfsg-3) ... Setting up python3-ipython (7.31.1-1) ... Setting up python3-sklearn (0.23.2-5ubuntu4) ... Setting up python3-pluggy (0.13.0-7.1) ... Setting up python3-pytest (6.2.5-1ubuntu2) ... Setting up python3-pil.imagetk:armhf (9.0.1-1) ... Setting up python3-ufolib2 (0.13.1+dfsg1-1) ... Setting up python3-fonttools (4.29.1-2build1) ... Setting up python3-pil:armhf (9.0.1-1) ... Setting up python3-matplotlib (3.5.1-2build1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-104-generic #118-Ubuntu SMP Wed Mar 2 19:03:41 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.38-3ubuntu1 dpkg-dev_1.21.1ubuntu1 g++-11_11.2.0-18ubuntu1 gcc-11_11.2.0-18ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.2.0-18ubuntu1 libstdc++6_12-20220313-1ubuntu1 linux-libc-dev_5.15.0-23.23 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.4.1 autoconf_2.71-2 automake_1:1.16.5-1.1ubuntu4 autopoint_0.21-4ubuntu3 autotools-dev_20220109.1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-6ubuntu1 binutils_2.38-3ubuntu1 binutils-arm-linux-gnueabihf_2.38-3ubuntu1 binutils-common_2.38-3ubuntu1 blt_2.5.3+dfsg-4.1build1 bsdextrautils_2.37.2-4ubuntu3 bsdutils_1:2.37.2-4ubuntu3 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-18ubuntu1 cython3_0.29.28-1ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79ubuntu1 debhelper_13.6ubuntu1 debianutils_5.5-1ubuntu1 debugedit_1:5.0-4 dh-autoreconf_20 dh-python_5.20220215 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu1 dpkg_1.21.1ubuntu1 dpkg-dev_1.21.1ubuntu1 dwz_0.14-1build1 e2fsprogs_1.46.5-2ubuntu1 fakeroot_1.28-1ubuntu1 file_1:5.41-2 findutils_4.8.0-1ubuntu2 fontconfig-config_2.13.1-4.2ubuntu4 fonts-dejavu-core_2.37-2build1 fonts-lyx_2.3.6-1 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-18ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-18ubuntu1 gcc-11-base_11.2.0-18ubuntu1 gcc-12-base_12-20220313-1ubuntu1 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-skbio Binary: python-skbio-doc, python3-skbio Architecture: any all Version: 0.5.6-6build1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Kevin Murray Homepage: https://github.com/biocore/scikit-bio Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/python-skbio Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), cython3, dh-python, python3-all-dev, python3-setuptools, python3-numpy (>= 1:1.9.2), python3-matplotlib, python3-cachecontrol, python3-decorator, python3-pandas (>= 0.19.2), python3-scipy (>= 1.3.3), python3-ipython, python3-hdmedians (>= 0.14.1), python3-sklearn, python3-natsort, libssw-dev, sphinx-common, libsimde-dev Build-Depends-Arch: python3-lockfile , python3-pytest Build-Depends-Indep: python3-sphinx , python3-sphinx-bootstrap-theme , python-numpy-doc , python3-doc , python-matplotlib-doc , python-scipy-doc , python-biom-format-doc , python-pandas-doc Package-List: python-skbio-doc deb doc optional arch=all profile=!nodoc python3-skbio deb python optional arch=any Checksums-Sha1: 53d9aca796ad7c38800a0cd3b359e6fbc205c0d6 8365758 python-skbio_0.5.6.orig.tar.gz a52dff4dc0fa49404ed2d8a8f5c70a6dcbc8bca6 17336 python-skbio_0.5.6-6build1.debian.tar.xz Checksums-Sha256: 69cf88626ff3803625aa65c7f6792f431318bd31f2b4d5c79e9a71cfc29c37ea 8365758 python-skbio_0.5.6.orig.tar.gz a0667bd8cd08d152d29eab2864328f03020dad655d26fecce886eabc48c4beae 17336 python-skbio_0.5.6-6build1.debian.tar.xz Files: 60d30db94b933863cf5a81eb6a9bcc9d 8365758 python-skbio_0.5.6.orig.tar.gz 3a3c4876c1a6c9a5958a42a42aacd19e 17336 python-skbio_0.5.6-6build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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signature ./python-skbio_0.5.6-6build1.dsc dpkg-source: info: extracting python-skbio in /<> dpkg-source: info: unpacking python-skbio_0.5.6.orig.tar.gz dpkg-source: info: unpacking python-skbio_0.5.6-6build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying mathjax-path dpkg-source: info: applying 0002-use-libsww-as-library-not-embedded-src.patch dpkg-source: info: applying no_privacy_breach_logo.patch dpkg-source: info: applying simde dpkg-source: info: applying soften_test dpkg-source: info: applying pandas1.1-ordination-fix.patch dpkg-source: info: applying pandas1.1-valueerror.patch dpkg-source: info: applying local_inventory dpkg-source: info: applying sphinx_add_javascript.patch dpkg-source: info: applying fix-dtype-precision-warnings.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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-23248678 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23248678 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23248678 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package python-skbio dpkg-buildpackage: info: source version 0.5.6-6build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' if [ "`find . -name "*.pyo"`" = "" ] ; then echo no need to clean up ; else dh_auto_clean; fi no need to clean up make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean find ./skbio -name '*.so' -delete find ./skbio -name '*.o' -delete rm -rf doc/build build doc/source/generated find doc -name *.doctree -delete rm -rf .pybuild rm -f scikit_bio.egg-info/PKG-INFO scikit_bio.egg-info/SOURCES.txt scikit_bio.egg-info/dependency_links.txt scikit_bio.egg-info/requires.txt scikit_bio.egg-info/top_level.txt rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c dh_auto_configure I: pybuild base:237: python3.10 setup.py config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/skbio/alignment/_ssw_wrapper.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: /<>/skbio/diversity/_phylogenetic.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: /<>/skbio/metadata/_intersection.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: /<>/skbio/stats/__subsample.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling skbio/metadata/_intersection.pyx because it changed. Compiling skbio/stats/__subsample.pyx because it changed. Compiling skbio/alignment/_ssw_wrapper.pyx because it changed. Compiling skbio/diversity/_phylogenetic.pyx because it changed. [1/4] Cythonizing skbio/alignment/_ssw_wrapper.pyx [2/4] Cythonizing skbio/diversity/_phylogenetic.pyx [3/4] Cythonizing skbio/metadata/_intersection.pyx [4/4] Cythonizing skbio/stats/__subsample.pyx running config make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>' dh_auto_build I: pybuild base:237: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.10_skbio/build/benchmarks copying benchmarks/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/benchmarks copying benchmarks/benchmarks.py -> /<>/.pybuild/cpython3_3.10_skbio/build/benchmarks creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio copying skbio/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio copying skbio/workflow.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio copying skbio/_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio copying skbio/test.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util copying skbio/util/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util copying skbio/util/_decorator.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util copying skbio/util/_misc.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util copying skbio/util/_exception.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util copying skbio/util/_testing.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util copying skbio/util/_warning.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/_fileobject.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/util.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/_exception.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/_warning.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/_iosources.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io copying skbio/io/registry.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata copying skbio/metadata/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata copying skbio/metadata/_mixin.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata copying skbio/metadata/_testing.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata copying skbio/metadata/_repr.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata copying skbio/metadata/_interval.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment copying skbio/alignment/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment copying skbio/alignment/_tabular_msa.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment copying skbio/alignment/_indexing.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment copying skbio/alignment/_repr.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment copying skbio/alignment/_pairwise.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity copying skbio/diversity/_block.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity copying skbio/diversity/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity copying skbio/diversity/_driver.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity copying skbio/diversity/_util.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_genetic_code.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_nucleotide_mixin.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_grammared_sequence.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_rna.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_protein.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_repr.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/distance.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_sequence.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence copying skbio/sequence/_dna.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tests copying skbio/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tests copying skbio/tests/test_workflow.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tests copying skbio/tests/test_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree copying skbio/tree/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree copying skbio/tree/_tree.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree copying skbio/tree/_majority_rule.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree copying skbio/tree/_exception.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree copying skbio/tree/_nj.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats copying skbio/stats/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats copying skbio/stats/_subsample.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats copying skbio/stats/gradient.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats copying skbio/stats/_misc.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats copying skbio/stats/power.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats copying skbio/stats/composition.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/tests copying skbio/util/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/tests copying skbio/util/tests/test_testing.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/tests copying skbio/util/tests/test_misc.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/tests copying skbio/util/tests/test_decorator.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/_sequence_feature_vocabulary.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/fasta.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/ordination.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/clustal.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/_blast.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/phylip.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/embl.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/lsmat.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/blast6.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/stockholm.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/gff3.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/genbank.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/blast7.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/emptyfile.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/qseq.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/fastq.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format copying skbio/io/format/newick.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests copying skbio/io/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests copying skbio/io/tests/test_util.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests copying skbio/io/tests/test_iosources.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests copying skbio/io/tests/test_registry.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_clustal.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_stockholm.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_blast6.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_sequence_feature_vocabulary.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_genbank.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_gff3.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_fasta.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_lsmat.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_qseq.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_blast7.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_newick.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_phylip.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_embl.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_emptyfile.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_fastq.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_ordination.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/test_interval.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/test_intersection.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/test_mixin.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_lib copying skbio/alignment/_lib/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_lib creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/test_tabular_msa.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/test_ssw.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/test_pairwise.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta copying skbio/diversity/beta/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta copying skbio/diversity/beta/_unifrac.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/test_util.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/test_block.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/test_driver.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_gini.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_faith_pd.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_lladser.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_ace.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_chao1.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests copying skbio/diversity/beta/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests copying skbio/diversity/beta/tests/test_unifrac.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_gini.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_faith_pd.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_ace.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_chao1.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_lladser.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_sequence.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_rna.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_nucleotide_sequences.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_protein.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_genetic_code.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_dna.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_distance.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_grammared_sequence.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree/tests copying skbio/tree/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree/tests copying skbio/tree/tests/test_tree.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree/tests copying skbio/tree/tests/test_majority_rule.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree/tests copying skbio/tree/tests/test_nj.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/tree/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/_mantel.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/_permanova.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/_anosim.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/_bioenv.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance copying skbio/stats/distance/_permdisp.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/evolve copying skbio/stats/evolve/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/evolve copying skbio/stats/evolve/_hommola.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/evolve creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_utils.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_correspondence_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_canonical_correspondence_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_principal_coordinate_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_redundancy_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_ordination_results.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests copying skbio/stats/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_subsample.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_misc.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_power.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_gradient.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_composition.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_anosim.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_mantel.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_base.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_permanova.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_permdisp.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_bioenv.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/evolve/tests copying skbio/stats/evolve/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/evolve/tests copying skbio/stats/evolve/tests/test_hommola.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/evolve/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_principal_coordinate_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_correspondence_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_util.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_redundancy_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_ordination_results.py -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/example_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/example_file.gz -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/real_file_2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/big5_file.bz2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/example_file.bz2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/big5_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/real_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/big5_file.gz -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/tests/data creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_as_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_single_seq_illumina1.3 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_single_record -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_sanger_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_dna -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blanks_end_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error12 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_mixed_qual_scores -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_upper -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_missing_locus_name -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_gc_data_length -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_5_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gf_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_multi_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_sequence -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_seq.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_6_ws_lines_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_dna_seq_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_del.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_zero_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_original_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_minimal -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error6 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_no_data -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_5_ws_lines_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_as_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_ws_lines_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_dna_3_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error9 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_10_fields -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_dna_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_multi_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_empty_str -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multi_line_tree_with_id -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_prot_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_vtab.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example2_scores -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq_roundtrip -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_header_too_short -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_multi_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_none -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_sequence -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_read -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_feature_level_record -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_middle -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_rn_tag -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_whitespace_only_lines -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_end_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_gc -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_references_mixed -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_original_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_sequence_names -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_multi_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_differing_fields -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_6_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_nuc_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error14 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_double_qual.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_footer -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_species -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_references -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_ws_line_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_as_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site_constraints -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_legacy_format -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_gibberish -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_extra -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_5_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_unit_sep.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error23 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_nonstring_labels -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example3_scores -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error8 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_blank_lines -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_lower -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_multi_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_empty_str -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive_mixed -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_minimal -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_last -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_msa -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_after_10_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_desc_mismatch -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_mixed_nans -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_seq_too_short -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_two_chunks -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_mixed_nans -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_header_too_long -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_unrecognized_field -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_in_seq_at_symbol -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gc_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_references -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_string -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error4 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_empty_str -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record_lower -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_rna_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_different_padding -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_max_width_1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_number_of_columns -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_sequence -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_nonexistent_gs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_null.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_nonexistent_gr -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_rna_seq_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_3 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_3_seqs_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_within_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_length_mismatch -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_too_many_columns -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_none -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq_roundtrip -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_single_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_filter -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_legacy_format -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_plus -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_multi_line_trees -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_original_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gs_no_whitespace -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_multi_char -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_invalid_too_many_columns -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_uniprot_record -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_for_sniffer -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_constructed -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_two_of_each_metadata -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_variable_length_ids -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_minimal -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_column_types -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_escape.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_no_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_short -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_original_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_tile -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_without_id -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_tab.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_multi_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_plus.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_bad_missing_directive -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_qual -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_gr -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_end_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blank_lines_between_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record_upper -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_max_width_5 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error7 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_w_beginning_whitespace -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_long -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_empty_str -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_single_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_prot_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_plus.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_plus -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_simple -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_id_mismatch -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_between_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_data_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multi_line_tree_no_id -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_6_ws_lines_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_line_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_qual.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_seq_too_long -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_blank_lines_between_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_x -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_tabular_msa_different_type -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_invalid_differing_fields -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_bio_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_single_seq_sanger -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_many_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_single_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_tree_ids -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_lane -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_prot_seq_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_whitespace_stripping -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_multi_record -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error21 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error19 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_multi_seq_illumina1.3 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_data_only -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_seq_sanger -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_feature_level_record_no_FT -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_as_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_bio_seq_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_multi_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_rna -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_single_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_10_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_reference -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error20 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_6_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error22 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_short_qual.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_line_within_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_space.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error11 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_bad_wrong_columns -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_multi_char -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_first -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_within_qual -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_blanks_end_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_diff_ids.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_no_qual.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_end_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_5 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_sanger_no_description -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_with_id -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error18 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_rna_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error16 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_between_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_all_data_types -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_between_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_seq_lengths -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_metadata_only -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_seq_data -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_no_data -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_zero_seq_len -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_for_sniffer_2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_PCoA_site -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf_with_whitespace -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_blank_lines -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_multi_char -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_bio_seq_non_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_species -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_6_blanks_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gs_with_whitespace -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_illumina1.3_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_single_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_and_blast7_default -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_negative -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_end_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_spaces.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/whitespace_only -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_w_beginning_whitespace -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_single_seq_illumina1.8 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error10 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gr_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_tabs.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_line_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_3_seqs_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error24 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gs_line -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_float -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_double_seq.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_data_type -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_trees -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error5 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error13 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_original_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error15 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_y -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_2_seqs_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_reference_items -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_8_fields -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_tabular_msa_different_type -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_prot_seqs_odd_labels -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/empty -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_seq.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error17 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error3 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_gr_data_length -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_qual.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_sanger_defaults -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_type_in_column -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_prot_seqs_odd_labels -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_long_qual.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_whitespace_only_lines -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_few_seqs -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/data creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/weighted_unifrac_dm.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/weighted_normalized_unifrac_dm.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/otu-table.tsv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/tree.nwk -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/unweighted_unifrac_dm.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/README.md -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/data creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/otu-table.tsv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/tree.nwk -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/faith-pd.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/README.md -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_out -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_data_raw -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_no_data_raw -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_no_data_out -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_wo_msg_out -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_w_msg_out -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_wo_msg_raw -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_data_out -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_real_out -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_w_msg_raw -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_raw -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_real_raw -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/data creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/moving_pictures_mf.tsv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_all_dms.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/moving_pictures_dm.tsv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm3.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/df_extra_column.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results_single_column.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results_different_column_order.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_dm_vegan.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm2.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/df.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm4.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_dm_dm2.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_duplicate_dms.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm_reordered.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/mantel_env_dm_vegan.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/mantel_veg_dm_vegan.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_exp_results_vegan.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_df_vegan.txt -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data creating /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_biplot_descriptors -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_Y -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_site_scaling2_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_fsvd_ref_3dim -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_species_scaling2_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_site_scaling1_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/varechem.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_biplot_projected_descriptors -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_Y -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_X -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_X -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_species_scaling1_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_site_scaling1_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_biplot_scaling1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/L&L_CA_data -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_sites_from_vegan.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/varespec.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_species_from_vegan.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_species_scaling1_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_12dim -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_propexpl_from_vegan.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/exp_PCoAzeros_site -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_eigh_ref_3dim -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_biplot_scaling2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_biplot_scaling2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_2 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_eigvals_from_vegan.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_constraints_from_vegan.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_site_scaling2_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/exp_PCoAEigenResults_site -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_species_scaling2_from_vegan -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_skbio -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_biplot_scaling1 -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_biplot_from_vegan.csv -> /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data running build_ext building 'skbio.metadata._intersection' extension creating build creating build/temp.linux-armhf-3.10 creating build/temp.linux-armhf-3.10/skbio creating build/temp.linux-armhf-3.10/skbio/metadata arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/include/python3.10 -c skbio/metadata/_intersection.c -o build/temp.linux-armhf-3.10/skbio/metadata/_intersection.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.10/skbio/metadata/_intersection.o -o /<>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/_intersection.cpython-310-arm-linux-gnueabihf.so building 'skbio.stats.__subsample' extension creating build/temp.linux-armhf-3.10/skbio/stats arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/python3.10 -c skbio/stats/__subsample.c -o build/temp.linux-armhf-3.10/skbio/stats/__subsample.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 skbio/stats/__subsample.c:714: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.10/skbio/stats/__subsample.o -o /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/__subsample.cpython-310-arm-linux-gnueabihf.so building 'skbio.alignment._ssw_wrapper' extension creating build/temp.linux-armhf-3.10/skbio/alignment arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iskbio/alignment -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.10 -c skbio/alignment/_ssw_wrapper.c -o build/temp.linux-armhf-3.10/skbio/alignment/_ssw_wrapper.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 skbio/alignment/_ssw_wrapper.c:720: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.10/skbio/alignment/_ssw_wrapper.o -lssw -o /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_ssw_wrapper.cpython-310-arm-linux-gnueabihf.so building 'skbio.diversity._phylogenetic' extension creating build/temp.linux-armhf-3.10/skbio/diversity arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/python3.10 -c skbio/diversity/_phylogenetic.c -o build/temp.linux-armhf-3.10/skbio/diversity/_phylogenetic.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 skbio/diversity/_phylogenetic.c:714: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.10/skbio/diversity/_phylogenetic.o -o /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/_phylogenetic.cpython-310-arm-linux-gnueabihf.so make[1]: Leaving directory '/<>' dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:237: cd /<>/.pybuild/cpython3_3.10_skbio/build; python3.10 -m pytest ============================= test session starts ============================== platform linux -- Python 3.10.3, pytest-6.2.5, py-1.10.0, pluggy-0.13.0 rootdir: /<> collected 2352 items skbio/alignment/tests/test_pairwise.py ......................... [ 1%] skbio/alignment/tests/test_ssw.py ........................... [ 2%] skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] ..............F......................................................... [ 6%] ........................................................................ [ 9%] ................................F....................................... [ 12%] ........................................................................ [ 15%] ........................................................................ [ 18%] ............ [ 19%] skbio/diversity/alpha/tests/test_ace.py .. [ 19%] skbio/diversity/alpha/tests/test_base.py ..............F......... [ 20%] skbio/diversity/alpha/tests/test_chao1.py ... [ 20%] skbio/diversity/alpha/tests/test_faith_pd.py FFF.FFFF [ 20%] skbio/diversity/alpha/tests/test_gini.py ... [ 21%] skbio/diversity/alpha/tests/test_lladser.py ..FF.....F.. [ 21%] skbio/diversity/beta/tests/test_unifrac.py .FFFFFFF.FFFFFFFF.FFFFF.FFFF [ 22%] skbio/diversity/tests/test_block.py F.......... [ 23%] skbio/diversity/tests/test_driver.py FFFF.FFFFF....F...FFF.......F...FF [ 24%] skbio/diversity/tests/test_util.py .........F [ 25%] skbio/io/format/tests/test_base.py ................................ [ 26%] skbio/io/format/tests/test_blast6.py ........... [ 26%] skbio/io/format/tests/test_blast7.py .............. [ 27%] skbio/io/format/tests/test_clustal.py ............. [ 28%] skbio/io/format/tests/test_embl.py ............................... [ 29%] skbio/io/format/tests/test_emptyfile.py .. [ 29%] skbio/io/format/tests/test_fasta.py .F.............. [ 30%] skbio/io/format/tests/test_fastq.py ............... [ 30%] skbio/io/format/tests/test_genbank.py ..................... [ 31%] skbio/io/format/tests/test_gff3.py ........................ [ 32%] skbio/io/format/tests/test_lsmat.py ....... [ 32%] skbio/io/format/tests/test_newick.py ....... [ 33%] skbio/io/format/tests/test_ordination.py ..... [ 33%] skbio/io/format/tests/test_phylip.py ....... [ 33%] skbio/io/format/tests/test_qseq.py ...... [ 34%] skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 34%] skbio/io/format/tests/test_stockholm.py ................................ [ 35%] ........................................... [ 37%] skbio/io/tests/test_iosources.py .......... [ 37%] skbio/io/tests/test_registry.py ........................................ [ 39%] ...................................................... [ 41%] skbio/io/tests/test_util.py .........................................sss [ 43%] sssssssssssssssssssssssssss............................................. [ 46%] ........................................................................ [ 49%] ................................ [ 51%] skbio/metadata/tests/test_intersection.py ............... [ 51%] skbio/metadata/tests/test_interval.py .................................. [ 53%] ..................................... [ 54%] skbio/metadata/tests/test_mixin.py ..................................... [ 56%] .......F..................................................... [ 58%] skbio/sequence/tests/test_distance.py .......................... [ 60%] skbio/sequence/tests/test_dna.py .... [ 60%] skbio/sequence/tests/test_genetic_code.py .......................... [ 61%] skbio/sequence/tests/test_grammared_sequence.py .....F.................. [ 62%] ................... [ 63%] skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 64%] ....... [ 64%] skbio/sequence/tests/test_protein.py .......... [ 64%] skbio/sequence/tests/test_rna.py .... [ 65%] skbio/sequence/tests/test_sequence.py .................................. [ 66%] ..........F............................................................. [ 69%] ....................F...................F...F..F.F.F...F.........F...... [ 72%] ....F........................................................F...F...... [ 75%] ....... [ 75%] skbio/stats/distance/tests/test_anosim.py .... [ 76%] skbio/stats/distance/tests/test_base.py ................................ [ 77%] ............................................................... [ 80%] skbio/stats/distance/tests/test_bioenv.py FFF.........FF... [ 80%] skbio/stats/distance/tests/test_mantel.py ................F.FFFFF.FFF... [ 82%] ......... [ 82%] skbio/stats/distance/tests/test_permanova.py .... [ 82%] skbio/stats/distance/tests/test_permdisp.py ............ [ 83%] skbio/stats/evolve/tests/test_hommola.py ............ [ 83%] skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 83%] ..... [ 83%] skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 84%] skbio/stats/ordination/tests/test_ordination_results.py ................ [ 84%] [ 84%] skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 85%] ...... [ 85%] skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 85%] skbio/stats/ordination/tests/test_util.py ......... [ 86%] skbio/stats/tests/test_composition.py .................................. [ 87%] ........................ [ 88%] skbio/stats/tests/test_gradient.py .......................... [ 89%] skbio/stats/tests/test_misc.py ... [ 89%] skbio/stats/tests/test_power.py ........................................ [ 91%] ... [ 91%] skbio/stats/tests/test_subsample.py .F..F.F...FF [ 92%] skbio/tests/test_base.py ..... [ 92%] skbio/tests/test_workflow.py ................. [ 92%] skbio/tree/tests/test_majority_rule.py ...... [ 93%] skbio/tree/tests/test_nj.py ........... [ 93%] skbio/tree/tests/test_tree.py .......................................... [ 95%] ................................................. [ 97%] skbio/util/tests/test_decorator.py ....................... [ 98%] skbio/util/tests/test_misc.py ................... [ 99%] skbio/util/tests/test_testing.py ............... [100%] =================================== FAILURES =================================== ________ TestTabularMSAPositionalMetadata.test_eq_from_different_source ________ self = def test_eq_from_different_source(self): obj1 = self._positional_metadata_constructor_( 3, positional_metadata={'foo': np.array([1, 2, 3])}) obj2 = self._positional_metadata_constructor_( 3, positional_metadata=pd.DataFrame({'foo': [1, 2, 3]}, index=['foo', 'bar', 'baz'])) > self.assertReallyEqual(obj1, obj2) skbio/metadata/_testing.py:464: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/util/_testing.py:31: in assertReallyEqual self.assertEqual(a, b) E AssertionError: Tabul[75 chars]: int32> E Stats: E sequence count: 1 E posi[38 chars]- E AAA != Tabul[75 chars]: int64> E Stats: E sequence count: 1 E posi[38 chars]- E AAA ____________________ TestILoc.test_fancy_empty_second_axis _____________________ self = def test_fancy_empty_second_axis(self): a = DNA("ACGT", metadata={0: 0}, positional_metadata={0: [1, 2, 3, 4]}) b = DNA("ACGT", metadata={1: 1}, positional_metadata={1: [1, 2, 3, 4]}) c = DNA("ACGT", metadata={2: 2}, positional_metadata={2: [1, 2, 3, 4]}) msa = TabularMSA([a, b, c], metadata={3: 3}, positional_metadata={3: [1, 2, 3, 4]}) > self.assertEqual(self.get(msa, (Ellipsis, [])), TabularMSA([a[0:0], b[0:0], c[0:0]], metadata={3: 3}, positional_metadata={3: np.array( [], dtype=int)})) E AssertionError: Tabul[86 chars]: int64> E Stats: E sequence count: 3 E posi[30 chars]----- != Tabul[86 chars]: int32> E Stats: E sequence count: 3 E posi[30 chars]----- skbio/alignment/tests/test_tabular_msa.py:1660: AssertionError _____________________ BaseTests.test_michaelis_menten_fit ______________________ self = def test_michaelis_menten_fit(self): > obs = michaelis_menten_fit([22]) skbio/diversity/alpha/tests/test_base.py:176: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_base.py:687: in michaelis_menten_fit ymtx[i] = np.asarray([observed_otus(subsample_counts(counts, n)) skbio/diversity/alpha/_base.py:687: in ymtx[i] = np.asarray([observed_otus(subsample_counts(counts, n)) skbio/stats/_subsample.py:246: in subsample_counts result = _subsample_counts_without_replacement(counts, n, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'int64_t' but got 'long' skbio/stats/__subsample.pyx:13: ValueError __________________________ FaithPDTests.test_faith_pd __________________________ self = def test_faith_pd(self): # expected results derived from QIIME 1.9.1, which # is a completely different implementation skbio's initial # phylogenetic diversity implementation > actual = faith_pd(self.b1[0], self.oids1, self.t1) skbio/diversity/alpha/tests/test_faith_pd.py:65: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ___________________ FaithPDTests.test_faith_pd_all_observed ____________________ self = def test_faith_pd_all_observed(self): > actual = faith_pd([1, 1, 1, 1, 1], self.oids1, self.t1) skbio/diversity/alpha/tests/test_faith_pd.py:51: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ____________________ FaithPDTests.test_faith_pd_extra_tips _____________________ self = def test_faith_pd_extra_tips(self): # results are the same despite presences of unobserved tips in tree > actual = faith_pd(self.b1[0], self.oids1, self.t1_w_extra_tips) skbio/diversity/alpha/tests/test_faith_pd.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ______________________ FaithPDTests.test_faith_pd_minimal ______________________ self = def test_faith_pd_minimal(self): # two tips tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;')) > actual = faith_pd([1, 0], ['OTU1', 'OTU2'], tree) skbio/diversity/alpha/tests/test_faith_pd.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ___________________ FaithPDTests.test_faith_pd_none_observed ___________________ self = def test_faith_pd_none_observed(self): > actual = faith_pd(np.array([], dtype=int), np.array([], dtype=int), self.t1) skbio/diversity/alpha/tests/test_faith_pd.py:41: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError __________________ FaithPDTests.test_faith_pd_qiime_tiny_test __________________ self = def test_faith_pd_qiime_tiny_test(self): # the following table and tree are derived from the QIIME 1.9.1 # "tiny-test" data tt_table_fp = get_data_path( os.path.join('qiime-191-tt', 'otu-table.tsv'), 'data') tt_tree_fp = get_data_path( os.path.join('qiime-191-tt', 'tree.nwk'), 'data') self.q_table = pd.read_csv(tt_table_fp, sep='\t', skiprows=1, index_col=0) self.q_tree = TreeNode.read(tt_tree_fp) expected_fp = get_data_path( os.path.join('qiime-191-tt', 'faith-pd.txt'), 'data') expected = pd.read_csv(expected_fp, sep='\t', index_col=0) for sid in self.q_table.columns: > actual = faith_pd(self.q_table[sid], otu_ids=self.q_table.index, tree=self.q_tree) skbio/diversity/alpha/tests/test_faith_pd.py:116: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________ FaithPDTests.test_faith_pd_root_not_observed _________________ self = def test_faith_pd_root_not_observed(self): # expected values computed by hand tree = TreeNode.read( StringIO('((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)' 'root;')) otu_ids = ['OTU%d' % i for i in range(1, 5)] # root node not observed, but branch between (OTU1, OTU2) and root # is considered observed > actual = faith_pd([1, 1, 0, 0], otu_ids, tree) skbio/diversity/alpha/tests/test_faith_pd.py:129: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________________ LladserTests.test_lladser_ci _________________________ self = def test_lladser_ci(self): """lladser_ci estimate using defaults contains p with 95% prob""" np.random.seed(12345678) reps = 100 sum = 0 for i in range(reps): > fake_obs, exp_p = create_fake_observation() skbio/diversity/alpha/tests/test_lladser.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/tests/test_lladser.py:31: in create_fake_observation fake_obs = subsample_counts(counts, 1000) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ counts = array([9000, 1, 1, ..., 1, 1, 1], dtype=int64), n = 1000 replace = False @experimental(as_of="0.4.0") def subsample_counts(counts, n, replace=False): """Randomly subsample from a vector of counts, with or without replacement. Parameters ---------- counts : 1-D array_like Vector of counts (integers) to randomly subsample from. n : int Number of items to subsample from `counts`. Must be less than or equal to the sum of `counts`. replace : bool, optional If ``True``, subsample with replacement. If ``False`` (the default), subsample without replacement. Returns ------- subsampled : ndarray Subsampled vector of counts where the sum of the elements equals `n` (i.e., ``subsampled.sum() == n``). Will have the same shape as `counts`. Raises ------ TypeError If `counts` cannot be safely converted to an integer datatype. ValueError If `n` is less than zero or greater than the sum of `counts` when `replace=False`. EfficiencyWarning If the accelerated code isn't present or hasn't been compiled. See Also -------- isubsample skbio.diversity.alpha Notes ----- If subsampling is performed without replacement (``replace=False``), a copy of `counts` is returned if `n` is equal to the number of items in `counts`, as all items will be chosen from the original vector. If subsampling is performed with replacement (``replace=True``) and `n` is equal to the number of items in `counts`, the subsampled vector that is returned may not necessarily be the same vector as `counts`. Examples -------- Subsample 4 items (without replacement) from a vector of counts: >>> import numpy as np >>> from skbio.stats import subsample_counts >>> a = np.array([4, 5, 0, 2, 1]) >>> sub = subsample_counts(a, 4) >>> sub.sum() 4 >>> sub.shape (5,) Trying to subsample an equal number of items (without replacement) results in the same vector as our input: >>> subsample_counts([0, 3, 0, 1], 4) array([0, 3, 0, 1]) Subsample 5 items (with replacement): >>> sub = subsample_counts([1, 0, 1, 2, 2, 3, 0, 1], 5, replace=True) >>> sub.sum() 5 >>> sub.shape (8,) """ if n < 0: raise ValueError("n cannot be negative.") counts = np.asarray(counts) > counts = counts.astype(int, casting='safe') E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' skbio/stats/_subsample.py:229: TypeError _______________________ LladserTests.test_lladser_ci_f3 ________________________ self = def test_lladser_ci_f3(self): """lladser_ci estimate using f=3 contains p with 95% prob""" # Test different values of f=3 and r=14, which lie exactly on the # 95% interval line. For 100 reps using simple cumulative binomial # probs we expect to have more than 5 misses of the interval in 38% # of all test runs. To make this test pass reliable we thus have to # set a defined seed np.random.seed(12345678) reps = 100 sum = 0 for i in range(reps): # re-create the obs for every estimate, such that they are truly # independent events > fake_obs, exp_p = create_fake_observation() skbio/diversity/alpha/tests/test_lladser.py:90: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/tests/test_lladser.py:31: in create_fake_observation fake_obs = subsample_counts(counts, 1000) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ counts = array([9000, 1, 1, ..., 1, 1, 1], dtype=int64), n = 1000 replace = False @experimental(as_of="0.4.0") def subsample_counts(counts, n, replace=False): """Randomly subsample from a vector of counts, with or without replacement. Parameters ---------- counts : 1-D array_like Vector of counts (integers) to randomly subsample from. n : int Number of items to subsample from `counts`. Must be less than or equal to the sum of `counts`. replace : bool, optional If ``True``, subsample with replacement. If ``False`` (the default), subsample without replacement. Returns ------- subsampled : ndarray Subsampled vector of counts where the sum of the elements equals `n` (i.e., ``subsampled.sum() == n``). Will have the same shape as `counts`. Raises ------ TypeError If `counts` cannot be safely converted to an integer datatype. ValueError If `n` is less than zero or greater than the sum of `counts` when `replace=False`. EfficiencyWarning If the accelerated code isn't present or hasn't been compiled. See Also -------- isubsample skbio.diversity.alpha Notes ----- If subsampling is performed without replacement (``replace=False``), a copy of `counts` is returned if `n` is equal to the number of items in `counts`, as all items will be chosen from the original vector. If subsampling is performed with replacement (``replace=True``) and `n` is equal to the number of items in `counts`, the subsampled vector that is returned may not necessarily be the same vector as `counts`. Examples -------- Subsample 4 items (without replacement) from a vector of counts: >>> import numpy as np >>> from skbio.stats import subsample_counts >>> a = np.array([4, 5, 0, 2, 1]) >>> sub = subsample_counts(a, 4) >>> sub.sum() 4 >>> sub.shape (5,) Trying to subsample an equal number of items (without replacement) results in the same vector as our input: >>> subsample_counts([0, 3, 0, 1], 4) array([0, 3, 0, 1]) Subsample 5 items (with replacement): >>> sub = subsample_counts([1, 0, 1, 2, 2, 3, 0, 1], 5, replace=True) >>> sub.sum() 5 >>> sub.shape (8,) """ if n < 0: raise ValueError("n cannot be negative.") counts = np.asarray(counts) > counts = counts.astype(int, casting='safe') E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' skbio/stats/_subsample.py:229: TypeError _________________________ LladserTests.test_lladser_pe _________________________ self = def test_lladser_pe(self): """lladser_pe returns point estimates within the expected variance""" obs = lladser_pe([3], r=4) self.assertTrue(np.isnan(obs)) np.random.seed(123456789) > fake_obs, exp_p = create_fake_observation() skbio/diversity/alpha/tests/test_lladser.py:45: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/tests/test_lladser.py:31: in create_fake_observation fake_obs = subsample_counts(counts, 1000) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ counts = array([9000, 1, 1, ..., 1, 1, 1], dtype=int64), n = 1000 replace = False @experimental(as_of="0.4.0") def subsample_counts(counts, n, replace=False): """Randomly subsample from a vector of counts, with or without replacement. Parameters ---------- counts : 1-D array_like Vector of counts (integers) to randomly subsample from. n : int Number of items to subsample from `counts`. Must be less than or equal to the sum of `counts`. replace : bool, optional If ``True``, subsample with replacement. If ``False`` (the default), subsample without replacement. Returns ------- subsampled : ndarray Subsampled vector of counts where the sum of the elements equals `n` (i.e., ``subsampled.sum() == n``). Will have the same shape as `counts`. Raises ------ TypeError If `counts` cannot be safely converted to an integer datatype. ValueError If `n` is less than zero or greater than the sum of `counts` when `replace=False`. EfficiencyWarning If the accelerated code isn't present or hasn't been compiled. See Also -------- isubsample skbio.diversity.alpha Notes ----- If subsampling is performed without replacement (``replace=False``), a copy of `counts` is returned if `n` is equal to the number of items in `counts`, as all items will be chosen from the original vector. If subsampling is performed with replacement (``replace=True``) and `n` is equal to the number of items in `counts`, the subsampled vector that is returned may not necessarily be the same vector as `counts`. Examples -------- Subsample 4 items (without replacement) from a vector of counts: >>> import numpy as np >>> from skbio.stats import subsample_counts >>> a = np.array([4, 5, 0, 2, 1]) >>> sub = subsample_counts(a, 4) >>> sub.sum() 4 >>> sub.shape (5,) Trying to subsample an equal number of items (without replacement) results in the same vector as our input: >>> subsample_counts([0, 3, 0, 1], 4) array([0, 3, 0, 1]) Subsample 5 items (with replacement): >>> sub = subsample_counts([1, 0, 1, 2, 2, 3, 0, 1], 5, replace=True) >>> sub.sum() 5 >>> sub.shape (8,) """ if n < 0: raise ValueError("n cannot be negative.") counts = np.asarray(counts) > counts = counts.astype(int, casting='safe') E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' skbio/stats/_subsample.py:229: TypeError ___________________ UnifracTests.test_unweighted_extra_tips ____________________ self = def test_unweighted_extra_tips(self): # UniFrac values are the same despite unobserved tips in the tree for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = unweighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1_w_extra_tips) skbio/diversity/beta/tests/test_unifrac.py:85: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError __________________ UnifracTests.test_unweighted_minimal_trees __________________ self = def test_unweighted_minimal_trees(self): # two tips tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;')) > actual = unweighted_unifrac([1, 0], [0, 0], ['OTU1', 'OTU2'], tree) skbio/diversity/beta/tests/test_unifrac.py:104: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ UnifracTests.test_unweighted_otus_out_of_order ________________ self = def test_unweighted_otus_out_of_order(self): # UniFrac API does not assert the observations are in tip order of the # input tree shuffled_ids = self.oids1[:] shuffled_b1 = self.b1.copy() shuffled_ids[0], shuffled_ids[-1] = shuffled_ids[-1], shuffled_ids[0] shuffled_b1[:, [0, -1]] = shuffled_b1[:, [-1, 0]] for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = unweighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:58: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ UnifracTests.test_unweighted_root_not_observed ________________ self = def test_unweighted_root_not_observed(self): # expected values computed with QIIME 1.9.1 and by hand # root node not observed, but branch between (OTU1, OTU2) and root # is considered shared > actual = unweighted_unifrac([1, 1, 0, 0], [1, 0, 0, 0], self.oids2, self.t2) skbio/diversity/beta/tests/test_unifrac.py:120: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _____________________ UnifracTests.test_unweighted_unifrac _____________________ self = def test_unweighted_unifrac(self): # expected results derived from QIIME 1.9.1, which # is a completely different implementation skbio's initial # unweighted unifrac implementation # sample A versus all > actual = unweighted_unifrac( self.b1[0], self.b1[1], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:338: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ UnifracTests.test_unweighted_unifrac_identity _________________ self = def test_unweighted_unifrac_identity(self): for i in range(len(self.b1)): > actual = unweighted_unifrac( self.b1[i], self.b1[i], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:174: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _____________ UnifracTests.test_unweighted_unifrac_non_overlapping _____________ self = def test_unweighted_unifrac_non_overlapping(self): # these communities only share the root node > actual = unweighted_unifrac( self.b1[4], self.b1[5], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:310: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ UnifracTests.test_unweighted_unifrac_symmetry _________________ self = def test_unweighted_unifrac_symmetry(self): for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = unweighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:182: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _______________ UnifracTests.test_unweighted_unifrac_zero_counts _______________ self = def test_unweighted_unifrac_zero_counts(self): > actual = unweighted_unifrac( [1, 1, 1, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:320: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ____________________ UnifracTests.test_weighted_extra_tips _____________________ self = def test_weighted_extra_tips(self): # UniFrac values are the same despite unobserved tips in the tree for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = weighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1_w_extra_tips) skbio/diversity/beta/tests/test_unifrac.py:95: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ___________________ UnifracTests.test_weighted_minimal_trees ___________________ self = def test_weighted_minimal_trees(self): # two tips tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;')) > actual = weighted_unifrac([1, 0], [0, 0], ['OTU1', 'OTU2'], tree) skbio/diversity/beta/tests/test_unifrac.py:112: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ___________ UnifracTests.test_weighted_normalized_root_not_observed ____________ self = def test_weighted_normalized_root_not_observed(self): # expected values computed by hand, these disagree with QIIME 1.9.1 # root node not observed, but branch between (OTU1, OTU2) and root # is considered shared > actual = weighted_unifrac([1, 0, 0, 0], [1, 1, 0, 0], self.oids2, self.t2, normalized=True) skbio/diversity/beta/tests/test_unifrac.py:160: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________ UnifracTests.test_weighted_otus_out_of_order _________________ self = def test_weighted_otus_out_of_order(self): # UniFrac API does not assert the observations are in tip order of the # input tree shuffled_ids = self.oids1[:] shuffled_b1 = self.b1.copy() shuffled_ids[0], shuffled_ids[-1] = shuffled_ids[-1], shuffled_ids[0] shuffled_b1[:, [0, -1]] = shuffled_b1[:, [-1, 0]] for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = weighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:75: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________ UnifracTests.test_weighted_root_not_observed _________________ self = def test_weighted_root_not_observed(self): # expected values computed by hand, these disagree with QIIME 1.9.1 # root node not observed, but branch between (OTU1, OTU2) and root # is considered shared > actual = weighted_unifrac([1, 0, 0, 0], [1, 1, 0, 0], self.oids2, self.t2) skbio/diversity/beta/tests/test_unifrac.py:144: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ______________________ UnifracTests.test_weighted_unifrac ______________________ self = def test_weighted_unifrac(self): # expected results derived from QIIME 1.9.1, which # is a completely different implementation skbio's initial # weighted unifrac implementation > actual = weighted_unifrac( self.b1[0], self.b1[1], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:450: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________ UnifracTests.test_weighted_unifrac_identity __________________ self = def test_weighted_unifrac_identity(self): for i in range(len(self.b1)): > actual = weighted_unifrac( self.b1[i], self.b1[i], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:405: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ____________ UnifracTests.test_weighted_unifrac_identity_normalized ____________ self = def test_weighted_unifrac_identity_normalized(self): for i in range(len(self.b1)): > actual = weighted_unifrac( self.b1[i], self.b1[i], self.oids1, self.t1, normalized=True) skbio/diversity/beta/tests/test_unifrac.py:517: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ______________ UnifracTests.test_weighted_unifrac_non_overlapping ______________ self = def test_weighted_unifrac_non_overlapping(self): # expected results derived from QIIME 1.9.1, which # is a completely different implementation skbio's initial # weighted unifrac implementation # these communities only share the root node > actual = weighted_unifrac( self.b1[4], self.b1[5], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:424: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________ UnifracTests.test_weighted_unifrac_non_overlapping_normalized _________ self = def test_weighted_unifrac_non_overlapping_normalized(self): # these communities only share the root node > actual = weighted_unifrac( self.b1[4], self.b1[5], self.oids1, self.t1, normalized=True) skbio/diversity/beta/tests/test_unifrac.py:535: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ UnifracTests.test_weighted_unifrac_normalized _________________ self = def test_weighted_unifrac_normalized(self): # expected results derived from QIIME 1.9.1, which # is a completely different implementation skbio's initial # weighted unifrac implementation > actual = weighted_unifrac( self.b1[0], self.b1[1], self.oids1, self.t1, normalized=True) skbio/diversity/beta/tests/test_unifrac.py:568: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________ UnifracTests.test_weighted_unifrac_symmetry __________________ self = def test_weighted_unifrac_symmetry(self): for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = weighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:413: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ____________ UnifracTests.test_weighted_unifrac_symmetry_normalized ____________ self = def test_weighted_unifrac_symmetry_normalized(self): for i in range(len(self.b1)): for j in range(len(self.b1)): > actual = weighted_unifrac( self.b1[i], self.b1[j], self.oids1, self.t1, normalized=True) skbio/diversity/beta/tests/test_unifrac.py:525: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ UnifracTests.test_weighted_unifrac_zero_counts ________________ self = def test_weighted_unifrac_zero_counts(self): > actual = weighted_unifrac( [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1) skbio/diversity/beta/tests/test_unifrac.py:430: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError __________ UnifracTests.test_weighted_unifrac_zero_counts_normalized ___________ self = def test_weighted_unifrac_zero_counts_normalized(self): # expected results derived from QIIME 1.9.1, which # is a completely different implementation skbio's initial # weighted unifrac implementation > actual = weighted_unifrac( [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1, normalized=True) skbio/diversity/beta/tests/test_unifrac.py:549: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac _setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate, skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _______________ ParallelBetaDiversity.test_block_beta_diversity ________________ self = def test_block_beta_diversity(self): > exp = beta_diversity('unweighted_unifrac', self.table1, self.sids1, tree=self.tree1, otu_ids=self.oids1) skbio/diversity/tests/test_block.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:354: in beta_diversity metric, counts_by_node = _setup_multiple_unweighted_unifrac( skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________________ AlphaDiversityTests.test_empty ________________________ self = def test_empty(self): # empty vector actual = alpha_diversity('observed_otus', np.array([], dtype=np.int64)) expected = pd.Series([0]) > assert_series_almost_equal(actual, expected) skbio/diversity/tests/test_driver.py:160: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = 0 0 dtype: int32, right = 0 0 dtype: int64 def assert_series_almost_equal(left, right): # pass all kwargs to ensure this function has consistent behavior even if # `assert_series_equal`'s defaults change > pdt.assert_series_equal(left, right, check_dtype=True, check_index_type=True, check_series_type=True, check_names=True, check_exact=False, check_datetimelike_compat=False, obj='Series') E AssertionError: Attributes of Series are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:322: AssertionError ______________________ AlphaDiversityTests.test_faith_pd _______________________ self = def test_faith_pd(self): # calling faith_pd through alpha_diversity gives same results as # calling it directly expected = [] for e in self.table1: > expected.append(faith_pd(e, tree=self.tree1, otu_ids=self.oids1)) skbio/diversity/tests/test_driver.py:235: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/alpha/_faith_pd.py:122: in faith_pd counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _____________________ AlphaDiversityTests.test_input_types _____________________ self = def test_input_types(self): list_result = alpha_diversity('observed_otus', [1, 3, 0, 1, 0]) array_result = alpha_diversity('observed_otus', np.array([1, 3, 0, 1, 0])) self.assertAlmostEqual(list_result[0], 3) assert_series_almost_equal(list_result, array_result) > list_result = alpha_diversity('faith_pd', [1, 3, 0, 1, 0], tree=self.tree1, otu_ids=self.oids1) skbio/diversity/tests/test_driver.py:210: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:169: in alpha_diversity counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ____________________ AlphaDiversityTests.test_invalid_input ____________________ self = def test_invalid_input(self): # number of ids doesn't match the number of samples self.assertRaises(ValueError, alpha_diversity, 'observed_otus', self.table1, list('ABC')) # unknown metric provided self.assertRaises(ValueError, alpha_diversity, 'not-a-metric', self.table1) # 3-D list provided as input self.assertRaises(ValueError, alpha_diversity, 'observed_otus', [[[43]]]) # negative counts self.assertRaises(ValueError, alpha_diversity, 'observed_otus', [0, 3, -12, 42]) # additional kwargs self.assertRaises(TypeError, alpha_diversity, 'observed_otus', [0, 1], not_a_real_kwarg=42.0) > self.assertRaises(TypeError, alpha_diversity, 'faith_pd', [0, 1], tree=self.tree1, otu_ids=['OTU1', 'OTU2'], not_a_real_kwarg=42.0) skbio/diversity/tests/test_driver.py:68: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:169: in alpha_diversity counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _______________________ AlphaDiversityTests.test_no_ids ________________________ self = def test_no_ids(self): # expected values hand-calculated expected = pd.Series([3, 3, 3, 3]) actual = alpha_diversity('observed_otus', self.table1) > assert_series_almost_equal(actual, expected) skbio/diversity/tests/test_driver.py:254: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = 0 3 1 3 2 3 3 3 dtype: int32 right = 0 3 1 3 2 3 3 3 dtype: int64 def assert_series_almost_equal(left, right): # pass all kwargs to ensure this function has consistent behavior even if # `assert_series_equal`'s defaults change > pdt.assert_series_equal(left, right, check_dtype=True, check_index_type=True, check_series_type=True, check_names=True, check_exact=False, check_datetimelike_compat=False, obj='Series') E AssertionError: Attributes of Series are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:322: AssertionError ____________________ AlphaDiversityTests.test_observed_otus ____________________ self = def test_observed_otus(self): # expected values hand-calculated expected = pd.Series([3, 3, 3, 3], index=self.sids1) actual = alpha_diversity('observed_otus', self.table1, self.sids1) > assert_series_almost_equal(actual, expected) skbio/diversity/tests/test_driver.py:221: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = A 3 B 3 C 3 D 3 dtype: int32 right = A 3 B 3 C 3 D 3 dtype: int64 def assert_series_almost_equal(left, right): # pass all kwargs to ensure this function has consistent behavior even if # `assert_series_equal`'s defaults change > pdt.assert_series_equal(left, right, check_dtype=True, check_index_type=True, check_series_type=True, check_names=True, check_exact=False, check_datetimelike_compat=False, obj='Series') E AssertionError: Attributes of Series are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:322: AssertionError ______________________ AlphaDiversityTests.test_optimized ______________________ self = def test_optimized(self): # calling optimized faith_pd gives same results as calling unoptimized # version > optimized = alpha_diversity('faith_pd', self.table1, tree=self.tree1, otu_ids=self.oids1) skbio/diversity/tests/test_driver.py:259: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:169: in alpha_diversity counts_by_node, branch_lengths = _setup_faith_pd( skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________ AlphaDiversityTests.test_single_count_vector _________________ self = def test_single_count_vector(self): actual = alpha_diversity('observed_otus', np.array([1, 0, 2])) expected = pd.Series([2]) > assert_series_almost_equal(actual, expected) skbio/diversity/tests/test_driver.py:197: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = 0 2 dtype: int32, right = 0 2 dtype: int64 def assert_series_almost_equal(left, right): # pass all kwargs to ensure this function has consistent behavior even if # `assert_series_equal`'s defaults change > pdt.assert_series_equal(left, right, check_dtype=True, check_index_type=True, check_series_type=True, check_names=True, check_exact=False, check_datetimelike_compat=False, obj='Series') E AssertionError: Attributes of Series are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:322: AssertionError __________________ BetaDiversityTests.test_alt_pairwise_func ___________________ self = def test_alt_pairwise_func(self): # confirm that pairwise_func is actually being used def not_a_real_pdist(counts, metric): return [[0.0, 42.0], [42.0, 0.0]] > dm1 = beta_diversity('unweighted_unifrac', self.table1, otu_ids=self.oids1, tree=self.tree1, pairwise_func=not_a_real_pdist) skbio/diversity/tests/test_driver.py:601: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:354: in beta_diversity metric, counts_by_node = _setup_multiple_unweighted_unifrac( skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ____________________ BetaDiversityTests.test_invalid_input _____________________ self = def test_invalid_input(self): # number of ids doesn't match the number of samples error_msg = (r"Number of rows") with self.assertRaisesRegex(ValueError, error_msg): beta_diversity(self.table1, list('AB'), 'euclidean') # unknown metric provided error_msg = r"not-a-metric" with self.assertRaisesRegex(ValueError, error_msg): beta_diversity('not-a-metric', self.table1) # 3-D list provided as input error_msg = (r"Only 1-D and 2-D") with self.assertRaisesRegex(ValueError, error_msg): beta_diversity('euclidean', [[[43]]]) # negative counts error_msg = r"negative values." with self.assertRaisesRegex(ValueError, error_msg): beta_diversity('euclidean', [[0, 1, 3, 4], [0, 3, -12, 42]]) with self.assertRaisesRegex(ValueError, error_msg): beta_diversity('euclidean', [[0, 1, 3, -4], [0, 3, 12, 42]]) # additional kwargs error_msg = r"keyword argument" with self.assertRaisesRegex(TypeError, error_msg): beta_diversity('euclidean', [[0, 1, 3], [0, 3, 12]], not_a_real_kwarg=42.0) with self.assertRaisesRegex(TypeError, error_msg): > beta_diversity('unweighted_unifrac', [[0, 1, 3], [0, 3, 12]], not_a_real_kwarg=42.0, tree=self.tree1, otu_ids=['O1', 'O2', 'O3']) skbio/diversity/tests/test_driver.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:354: in beta_diversity metric, counts_by_node = _setup_multiple_unweighted_unifrac( skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError __________________ BetaDiversityTests.test_unweighted_unifrac __________________ self = def test_unweighted_unifrac(self): # TODO: update npt.assert_almost_equal calls to use DistanceMatrix # near-equality testing when that support is available # expected values calculated by hand > dm1 = beta_diversity('unweighted_unifrac', self.table1, self.sids1, otu_ids=self.oids1, tree=self.tree1) skbio/diversity/tests/test_driver.py:528: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:354: in beta_diversity metric, counts_by_node = _setup_multiple_unweighted_unifrac( skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ___________________ BetaDiversityTests.test_weighted_unifrac ___________________ self = def test_weighted_unifrac(self): # TODO: update npt.assert_almost_equal calls to use DistanceMatrix # near-equality testing when that support is available # expected values calculated by hand > dm1 = beta_diversity('weighted_unifrac', self.table1, self.sids1, otu_ids=self.oids1, tree=self.tree1) skbio/diversity/tests/test_driver.py:547: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:363: in beta_diversity metric, counts_by_node = _setup_multiple_weighted_unifrac( skbio/diversity/beta/_unifrac.py:521: in _setup_multiple_weighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _____________ BetaDiversityTests.test_weighted_unifrac_normalized ______________ self = def test_weighted_unifrac_normalized(self): # TODO: update npt.assert_almost_equal calls to use DistanceMatrix # near-equality testing when that support is available # expected values calculated by hand > dm1 = beta_diversity('weighted_unifrac', self.table1, self.sids1, otu_ids=self.oids1, tree=self.tree1, normalized=True) skbio/diversity/tests/test_driver.py:567: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_driver.py:363: in beta_diversity metric, counts_by_node = _setup_multiple_weighted_unifrac( skbio/diversity/beta/_unifrac.py:521: in _setup_multiple_weighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ______________ TestPartialBetaDiversity.test_id_pairs_as_iterable ______________ self = def test_id_pairs_as_iterable(self): id_pairs = iter([('B', 'C'), ]) > dm = partial_beta_diversity('unweighted_unifrac', self.table1, self.sids1, otu_ids=self.oids1, tree=self.tree1, id_pairs=id_pairs) skbio/diversity/tests/test_driver.py:670: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ :2: in partial_beta_diversity ??? skbio/util/_decorator.py:260: in wrapped_f return func(*args[1:], **kwargs) skbio/diversity/_driver.py:250: in partial_beta_diversity metric, counts_by_node = _setup_multiple_unweighted_unifrac( skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ___________ TestPartialBetaDiversity.test_unweighted_unifrac_partial ___________ self = def test_unweighted_unifrac_partial(self): # TODO: update npt.assert_almost_equal calls to use DistanceMatrix # near-equality testing when that support is available # expected values calculated by hand > dm = partial_beta_diversity('unweighted_unifrac', self.table1, self.sids1, otu_ids=self.oids1, tree=self.tree1, id_pairs=[('B', 'C'), ]) skbio/diversity/tests/test_driver.py:689: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ :2: in partial_beta_diversity ??? skbio/util/_decorator.py:260: in wrapped_f return func(*args[1:], **kwargs) skbio/diversity/_driver.py:250: in partial_beta_diversity metric, counts_by_node = _setup_multiple_unweighted_unifrac( skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________ TestPartialBetaDiversity.test_weighted_unifrac_partial_full __________ self = def test_weighted_unifrac_partial_full(self): # TODO: update npt.assert_almost_equal calls to use DistanceMatrix # near-equality testing when that support is available # expected values calculated by hand > dm1 = partial_beta_diversity('weighted_unifrac', self.table1, self.sids1, otu_ids=self.oids1, tree=self.tree1, id_pairs=[('A', 'B'), ('A', 'C'), ('B', 'C')]) skbio/diversity/tests/test_driver.py:706: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ :2: in partial_beta_diversity ??? skbio/util/_decorator.py:260: in wrapped_f return func(*args[1:], **kwargs) skbio/diversity/_driver.py:259: in partial_beta_diversity metric, counts_by_node = _setup_multiple_weighted_unifrac( skbio/diversity/beta/_unifrac.py:521: in _setup_multiple_weighted_unifrac _setup_multiple_unifrac(counts, otu_ids, tree, validate) skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac _vectorize_counts_and_tree(counts, otu_ids, tree) skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError ________________ ValidationTests.test_vectorize_counts_and_tree ________________ self = def test_vectorize_counts_and_tree(self): t = TreeNode.read(io.StringIO("((a:1, b:2)c:3)root;")) counts = np.array([[0, 1], [1, 5], [10, 1]]) count_array, indexed, branch_lengths = \ > _vectorize_counts_and_tree(counts, np.array(['a', 'b']), t) skbio/diversity/tests/test_util.py:249: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/diversity/_util.py:130: in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' skbio/diversity/_phylogenetic.pyx:184: ValueError _________________________ SnifferTests.test_positives __________________________ self = def test_positives(self): for fp in self.positive_fps: > self.assertEqual(_fasta_sniffer(fp), (True, {})) E AssertionError: Tuples differ: (False, {}) != (True, {}) E E First differing element 0: E False E True E E - (False, {}) E + (True, {}) skbio/io/format/tests/test_fasta.py:153: AssertionError __________ TestPositionalMetadataMixin.test_eq_from_different_source ___________ self = def test_eq_from_different_source(self): obj1 = self._positional_metadata_constructor_( 3, positional_metadata={'foo': np.array([1, 2, 3])}) obj2 = self._positional_metadata_constructor_( 3, positional_metadata=pd.DataFrame({'foo': [1, 2, 3]}, index=['foo', 'bar', 'baz'])) > self.assertReallyEqual(obj1, obj2) skbio/metadata/_testing.py:464: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/util/_testing.py:31: in assertReallyEqual self.assertEqual(a, b) E AssertionError: .ExamplePositionalMetadataMixin object at 0xef0beb38> != .ExamplePositionalMetadataMixin object at 0xef0be238> _______________________ TestGrammaredSequence.test_degap _______________________ self = def test_degap(self): kw = { 'metadata': { 'id': 'some_id', 'description': 'some description', }, } self.assertEqual( ExampleGrammaredSequence( "", positional_metadata={'qual': []}, **kw).degap(), ExampleGrammaredSequence( "", positional_metadata={'qual': []}, **kw)) self.assertEqual( ExampleGrammaredSequence( "ABCXYZ", positional_metadata={'qual': np.arange(6)}, **kw).degap(), ExampleGrammaredSequence( "ABCXYZ", positional_metadata={'qual': np.arange(6)}, **kw)) > self.assertEqual( ExampleGrammaredSequence( "ABC-XYZ", positional_metadata={'qual': np.arange(7)}, **kw).degap(), ExampleGrammaredSequence( "ABCXYZ", positional_metadata={'qual': [0, 1, 2, 4, 5, 6]}, **kw)) E AssertionError: Examp[165 chars]: int32> E Stats: E length: 6 E has gaps: Fa[95 chars]BCXYZ != Examp[165 chars]: int64> E Stats: E length: 6 E has gaps: Fa[95 chars]BCXYZ skbio/sequence/tests/test_grammared_sequence.py:525: AssertionError _________ TestSequencePositionalMetadata.test_eq_from_different_source _________ self = def test_eq_from_different_source(self): obj1 = self._positional_metadata_constructor_( 3, positional_metadata={'foo': np.array([1, 2, 3])}) obj2 = self._positional_metadata_constructor_( 3, positional_metadata=pd.DataFrame({'foo': [1, 2, 3]}, index=['foo', 'bar', 'baz'])) > self.assertReallyEqual(obj1, obj2) skbio/metadata/_testing.py:464: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/util/_testing.py:31: in assertReallyEqual self.assertEqual(a, b) E AssertionError: Seque[66 chars]pe: int32> E Stats: E length: 3 E ------------------------- E 0 ZZZ != Seque[66 chars]pe: int64> E Stats: E length: 3 E ------------------------- E 0 ZZZ _____ TestSequence.test_eq_sequences_from_different_sources_compare_equal ______ self = def test_eq_sequences_from_different_sources_compare_equal(self): # sequences that have the same data but are constructed from different # types of data should compare equal im = IntervalMetadata(4) im.add([(0, 2)], metadata={'gene': 'sagB'}) seq1 = Sequence('ACGT', metadata={'id': 'foo', 'desc': 'abc'}, positional_metadata={'quality': (1, 2, 3, 4)}, interval_metadata=im) seq2 = Sequence(np.array([65, 67, 71, 84], dtype=np.uint8), metadata={'id': 'foo', 'desc': 'abc'}, positional_metadata={'quality': np.array([1, 2, 3, 4])}, interval_metadata=im) > self.assertTrue(seq1 == seq2) E AssertionError: False is not true skbio/sequence/tests/test_sequence.py:622: AssertionError ____________ TestSequence.test_getitem_with_boolean_vector_has_qual ____________ self = def test_getitem_with_boolean_vector_has_qual(self): s = "0123456789abcdef" length = len(s) seq = Sequence(s, metadata={'id': 'id11', 'description': 'dsc11'}, positional_metadata={'quality': np.arange(length)}) eseq = Sequence("13579bdf", metadata={'id': 'id11', 'description': 'dsc11'}, positional_metadata={'quality': [1, 3, 5, 7, 9, 11, 13, 15]}) > self.assertEqual(seq[np.array([False, True] * 8)], eseq) E AssertionError: Seque[130 chars]: int32> E Stats: E length: 8 E ----------------[19 chars]79bdf != Seque[130 chars]: int64> E Stats: E length: 8 E ----------------[19 chars]79bdf skbio/sequence/tests/test_sequence.py:932: AssertionError __________ TestSequence.test_getitem_with_int_has_positional_metadata __________ self = def test_getitem_with_int_has_positional_metadata(self): s = "Sequence string !1@2#3?.," length = len(s) seq = Sequence(s, metadata={'id': 'id', 'description': 'dsc'}, positional_metadata={'quality': np.arange(length)}) eseq = Sequence("S", {'id': 'id', 'description': 'dsc'}, positional_metadata={'quality': np.array([0])}) self.assertEqual(seq[0], eseq) eseq = Sequence(",", metadata={'id': 'id', 'description': 'dsc'}, positional_metadata={'quality': np.array([len(seq) - 1])}) self.assertEqual(seq[len(seq) - 1], eseq) eseq = Sequence("t", metadata={'id': 'id', 'description': 'dsc'}, positional_metadata={'quality': [10]}) > self.assertEqual(seq[10], eseq) E AssertionError: Seque[126 chars]: int32> E Stats: E length: 1 E ----------------------------- E 0 t != Seque[126 chars]: int64> E Stats: E length: 1 E ----------------------------- E 0 t skbio/sequence/tests/test_sequence.py:689: AssertionError ___ TestSequence.test_getitem_with_iterable_of_mixed_has_positional_metadata ___ self = def test_getitem_with_iterable_of_mixed_has_positional_metadata(self): s = "0123456789abcdef" length = len(s) seq = Sequence(s, metadata={'id': 'id7', 'description': 'dsc7'}, positional_metadata={'quality': np.arange(length)}) def generator(): yield slice(0, 4) yield slice(200, 400) yield -1 yield slice(-2, -4, -1) yield 9 eseq = Sequence("0123fed9", metadata={'id': 'id7', 'description': 'dsc7'}, positional_metadata={'quality': [0, 1, 2, 3, 15, 14, 13, 9]}) > self.assertEqual(seq[[0, 1, 2, 3, 15, 14, 13, 9]], eseq) E AssertionError: Seque[128 chars]: int32> E Stats: E length: 8 E ----------------[19 chars]3fed9 != Seque[128 chars]: int64> E Stats: E length: 8 E ----------------[19 chars]3fed9 skbio/sequence/tests/test_sequence.py:853: AssertionError ______ TestSequence.test_getitem_with_numpy_index_has_positional_metadata ______ self = def test_getitem_with_numpy_index_has_positional_metadata(self): s = "0123456789abcdef" length = len(s) seq = Sequence(s, metadata={'id': 'id9', 'description': 'dsc9'}, positional_metadata={'quality': np.arange(length)}) eseq = Sequence("0123fed9", metadata={'id': 'id9', 'description': 'dsc9'}, positional_metadata={'quality': [0, 1, 2, 3, 15, 14, 13, 9]}) > self.assertEqual(seq[np.array([0, 1, 2, 3, 15, 14, 13, 9])], eseq) E AssertionError: Seque[128 chars]: int32> E Stats: E length: 8 E ----------------[19 chars]3fed9 != Seque[128 chars]: int64> E Stats: E length: 8 E ----------------[19 chars]3fed9 skbio/sequence/tests/test_sequence.py:887: AssertionError _________ TestSequence.test_getitem_with_slice_has_positional_metadata _________ self = def test_getitem_with_slice_has_positional_metadata(self): s = "0123456789abcdef" length = len(s) seq = Sequence(s, metadata={'id': 'id3', 'description': 'dsc3'}, positional_metadata={'quality': np.arange(length)}) eseq = Sequence("012", metadata={'id': 'id3', 'description': 'dsc3'}, positional_metadata={'quality': np.arange(3)}) self.assertEqual(seq[0:3], eseq) self.assertEqual(seq[:3], eseq) self.assertEqual(seq[:3:1], eseq) eseq = Sequence("def", metadata={'id': 'id3', 'description': 'dsc3'}, positional_metadata={'quality': [13, 14, 15]}) > self.assertEqual(seq[-3:], eseq) E AssertionError: Seque[128 chars]: int32> E Stats: E length: 3 E ----------------[14 chars]0 def != Seque[128 chars]: int64> E Stats: E length: 3 E ----------------[14 chars]0 def skbio/sequence/tests/test_sequence.py:747: AssertionError ____ TestSequence.test_getitem_with_tuple_of_mixed_with_positional_metadata ____ self = def test_getitem_with_tuple_of_mixed_with_positional_metadata(self): s = "0123456789abcdef" length = len(s) seq = Sequence(s, metadata={'id': 'id5', 'description': 'dsc5'}, positional_metadata={'quality': np.arange(length)}) eseq = Sequence("00000", metadata={'id': 'id5', 'description': 'dsc5'}, positional_metadata={'quality': [0, 0, 0, 0, 0]}) > self.assertEqual(seq[0, 0, 0, 0, 0], eseq) E AssertionError: Seque[128 chars]: int32> E Stats: E length: 5 E ----------------[16 chars]00000 != Seque[128 chars]: int64> E Stats: E length: 5 E ----------------[16 chars]00000 skbio/sequence/tests/test_sequence.py:803: AssertionError ___________________ TestSequence.test_init_invalid_sequence ____________________ TypeError: Can cannot create a sequence with 'int32' During handling of the above exception, another exception occurred: self = def test_init_invalid_sequence(self): # invalid dtype (numpy.ndarray input) with self.assertRaises(TypeError): # int64 Sequence(np.array([1, 2, 3])) with self.assertRaises(TypeError): # |S21 Sequence(np.array([1, "23", 3])) with self.assertRaises(TypeError): # object Sequence(np.array([1, {}, ()])) # invalid input type (non-numpy.ndarray input) with self.assertRaisesRegex(TypeError, r'tuple'): Sequence(('a', 'b', 'c')) with self.assertRaisesRegex(TypeError, r'list'): Sequence(['a', 'b', 'c']) with self.assertRaisesRegex(TypeError, r'set'): Sequence({'a', 'b', 'c'}) with self.assertRaisesRegex(TypeError, r'dict'): Sequence({'a': 42, 'b': 43, 'c': 44}) with self.assertRaisesRegex(TypeError, r'int'): Sequence(42) with self.assertRaisesRegex(TypeError, r'float'): Sequence(4.2) > with self.assertRaisesRegex(TypeError, r'int64'): E AssertionError: "int64" does not match "Can cannot create a sequence with 'int32'" skbio/sequence/tests/test_sequence.py:476: AssertionError ________________ TestSequence.test_iter_has_positional_metadata ________________ self = def test_iter_has_positional_metadata(self): tested = False seq = Sequence("0123456789", metadata={'id': 'a', 'desc': 'b'}, positional_metadata={'qual': np.arange(10)}) for i, s in enumerate(seq): tested = True > self.assertEqual(s, Sequence(str(i), metadata={'id': 'a', 'desc': 'b'}, positional_metadata={'qual': [i]})) E AssertionError: Seque[107 chars]ype: int32> E Stats: E length: 1 E -------------------------- E 0 0 != Seque[107 chars]ype: int64> E Stats: E length: 1 E -------------------------- E 0 0 skbio/sequence/tests/test_sequence.py:1036: AssertionError ______________ TestSequence.test_reversed_has_positional_metadata ______________ self = def test_reversed_has_positional_metadata(self): tested = False seq = Sequence("0123456789", metadata={'id': 'a', 'desc': 'b'}, positional_metadata={'qual': np.arange(10)}) for i, s in enumerate(reversed(seq)): tested = True > self.assertEqual(s, Sequence(str(9 - i), metadata={'id': 'a', 'desc': 'b'}, positional_metadata={'qual': [9 - i]})) E AssertionError: Seque[107 chars]ype: int32> E Stats: E length: 1 E -------------------------- E 0 9 != Seque[107 chars]ype: int64> E Stats: E length: 1 E -------------------------- E 0 9 skbio/sequence/tests/test_sequence.py:1056: AssertionError _________________ TestSequence.test_slice_positional_metadata __________________ self = def test_slice_positional_metadata(self): seq = Sequence('ABCDEFGHIJ', positional_metadata={'foo': np.arange(10), 'bar': np.arange(100, 110)}) > self.assertTrue(pd.DataFrame({'foo': [0], 'bar': [100]}).equals( seq._slice_positional_metadata(0))) E AssertionError: False is not true skbio/sequence/tests/test_sequence.py:715: AssertionError _________________ BIOENVTests.test_bioenv_all_columns_explicit _________________ self = def test_bioenv_all_columns_explicit(self): # Test with all columns being specified. obs = bioenv(self.dm, self.df, columns=self.cols) > assert_data_frame_almost_equal(obs, self.exp_results) skbio/stats/distance/tests/test_bioenv.py:102: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = size correlation vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143 TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286 right = size correlation vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143 TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286 rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _________________ BIOENVTests.test_bioenv_all_columns_implicit _________________ self = def test_bioenv_all_columns_implicit(self): # Test with all columns in data frame (implicitly). obs = bioenv(self.dm, self.df) > assert_data_frame_almost_equal(obs, self.exp_results) skbio/stats/distance/tests/test_bioenv.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = size correlation vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143 TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286 right = size correlation vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143 TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286 rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ________________ BIOENVTests.test_bioenv_different_column_order ________________ self = def test_bioenv_different_column_order(self): # Specifying columns in a different order will change the row labels in # the results data frame as the column subsets will be reordered, but # the actual results (e.g., correlation coefficients) shouldn't change. obs = bioenv(self.dm, self.df, columns=self.cols[::-1]) > assert_data_frame_almost_equal( obs, self.exp_results_different_column_order) skbio/stats/distance/tests/test_bioenv.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = size correlation vars ... PH, ANNUAL_SEASON_PRECPT, ... 10 0.607143 LATITUDE, LONGITUDE, CMIN_RATE, PH, ANNUAL_SEAS... 11 0.539286 right = size correlation vars ... PH, ANNUAL_SEASON_PRECPT, ... 10 0.607143 LATITUDE, LONGITUDE, CMIN_RATE, PH, ANNUAL_SEAS... 11 0.539286 rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ____________________ BIOENVTests.test_bioenv_single_column _____________________ self = def test_bioenv_single_column(self): obs = bioenv(self.dm, self.df, columns=['PH']) > assert_data_frame_almost_equal(obs, self.exp_results_single_column) skbio/stats/distance/tests/test_bioenv.py:112: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = size correlation vars PH 1 0.75 right = size correlation vars PH 1 0.75 rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ____________________ BIOENVTests.test_bioenv_vegan_example _____________________ self = def test_bioenv_vegan_example(self): # The correlation coefficient in the first row of the # results (rho=0.2516) is different from the correlation coefficient # computed by vegan (rho=0.2513). This seems to occur due to # differences in numerical precision when calculating the Euclidean # distances, which affects the rank calculations in Spearman # (specifically, dealing with ties). The ranked distances end up being # slightly different between vegan and our implementation because some # distances are treated as ties in vegan but treated as distinct values # in our implementation. This explains the difference in rho values. I # verified that using Pearson correlation instead of Spearman on the # same distances yields *very* similar results. Thus, the discrepancy # seems to stem from differences when computing ranks/ties. obs = bioenv(self.dm_vegan, self.df_vegan) > assert_data_frame_almost_equal(obs, self.exp_results_vegan, rtol=1e-3) skbio/stats/distance/tests/test_bioenv.py:149: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = size correlation vars P 1...l 4 0.361875 log(N), P, Ca, pH, Al 5 0.321552 log(N), P, K, Ca, pH, Al 6 0.282181 right = size correlation vars P 1...l 4 0.361875 log(N), P, Ca, pH, Al 5 0.321552 log(N), P, K, Ca, pH, Al 6 0.282181 rtol = 0.001 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ____________________ PairwiseMantelTests.test_duplicate_dms ____________________ self = def test_duplicate_dms(self): obs = pwmantel((self.minx_dm, self.minx_dm, self.minx_dm), alternative='less') > assert_data_frame_almost_equal(obs, self.exp_results_duplicate_dms) skbio/stats/distance/tests/test_mantel.py:376: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ... 1.0 1.0 3 pearson 999 less 1 2 1.0 1.0 3 pearson 999 less right = statistic p-value n method permutations alternative dm1 dm2 ... 1.0 1.0 3 pearson 999 less 1 2 1.0 1.0 3 pearson 999 less rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _________________ PairwiseMantelTests.test_filepaths_as_input __________________ self = def test_filepaths_as_input(self): dms = [ get_data_path('dm.txt'), get_data_path('dm2.txt'), ] np.random.seed(0) obs = pwmantel(dms) > assert_data_frame_almost_equal(obs, self.exp_results_dm_dm2) skbio/stats/distance/tests/test_mantel.py:465: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 0 1 0.702031 0.001 6 pearson 999 two-sided right = statistic p-value n method permutations alternative dm1 dm2 0 1 0.702031 0.001 6 pearson 999 two-sided rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ______________________ PairwiseMantelTests.test_id_lookup ______________________ self = def test_id_lookup(self): # Matrices have mismatched IDs but a lookup is provided. self.minx_dm_extra.ids = ['a', 'b', 'c', 'foo'] self.minz_dm_extra.ids = ['d', 'e', 'f', 'bar'] lookup = {'a': '0', 'b': '1', 'c': '2', 'foo': 'foo', 'd': '0', 'e': '1', 'f': '2', 'bar': 'bar', '0': '0', '1': '1', '2': '2'} x = self.minx_dm_extra.filter(['b', 'a', 'foo', 'c']) y = self.miny_dm.filter(['0', '2', '1']) z = self.minz_dm_extra.filter(['bar', 'e', 'f', 'd']) x_copy = x.copy() y_copy = y.copy() z_copy = z.copy() np.random.seed(0) obs = pwmantel((x, y, z), alternative='greater', strict=False, lookup=lookup) > assert_data_frame_almost_equal( obs, self.exp_results_reordered_distance_matrices) skbio/stats/distance/tests/test_mantel.py:431: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.822 3 pearson 999 greater right = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.822 3 pearson 999 greater rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _______________ PairwiseMantelTests.test_many_filepaths_as_input _______________ self = def test_many_filepaths_as_input(self): dms = [ get_data_path('dm2.txt'), get_data_path('dm.txt'), get_data_path('dm4.txt'), get_data_path('dm3.txt') ] np.random.seed(0) obs = pwmantel(dms) > assert_data_frame_almost_equal(obs, self.exp_results_all_dms) skbio/stats/distance/tests/test_mantel.py:477: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ...920688 0.004 6 pearson 999 two-sided 2 3 0.717297 0.003 6 pearson 999 two-sided right = statistic p-value n method permutations alternative dm1 dm2 ...920688 0.004 6 pearson 999 two-sided 2 3 0.717297 0.003 6 pearson 999 two-sided rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ______________ PairwiseMantelTests.test_minimal_compatible_input _______________ self = def test_minimal_compatible_input(self): # Matrices are already in the correct order and have matching IDs. np.random.seed(0) # input as DistanceMatrix instances obs = pwmantel(self.min_dms, alternative='greater') > assert_data_frame_almost_equal(obs, self.exp_results_minimal) skbio/stats/distance/tests/test_mantel.py:355: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.835 3 pearson 999 greater right = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.835 3 pearson 999 greater rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError ________ PairwiseMantelTests.test_minimal_compatible_input_with_labels _________ self = def test_minimal_compatible_input_with_labels(self): np.random.seed(0) obs = pwmantel(self.min_dms, alternative='greater', labels=('minx', 'miny', 'minz')) > assert_data_frame_almost_equal( obs, self.exp_results_minimal_with_labels) skbio/stats/distance/tests/test_mantel.py:369: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ...9743 1.000 3 pearson 999 greater miny minz -0.841698 0.835 3 pearson 999 greater right = statistic p-value n method permutations alternative dm1 dm2 ...9743 1.000 3 pearson 999 greater miny minz -0.841698 0.835 3 pearson 999 greater rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _____________________ PairwiseMantelTests.test_na_p_value ______________________ self = def test_na_p_value(self): obs = pwmantel((self.miny_dm, self.minx_dm), method='spearman', permutations=0) > assert_data_frame_almost_equal(obs, self.exp_results_na_p_value) skbio/stats/distance/tests/test_mantel.py:381: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 0 1 0.5 NaN 3 spearman 0 two-sided right = statistic p-value n method permutations alternative dm1 dm2 0 1 0.5 NaN 3 spearman 0 two-sided rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _____________ PairwiseMantelTests.test_reordered_distance_matrices _____________ self = def test_reordered_distance_matrices(self): # Matrices have matching IDs but they all have different ordering. x = self.minx_dm.filter(['1', '0', '2']) y = self.miny_dm.filter(['0', '2', '1']) z = self.minz_dm.filter(['1', '2', '0']) np.random.seed(0) obs = pwmantel((x, y, z), alternative='greater') > assert_data_frame_almost_equal( obs, self.exp_results_reordered_distance_matrices) skbio/stats/distance/tests/test_mantel.py:392: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.822 3 pearson 999 greater right = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.822 3 pearson 999 greater rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _______________________ PairwiseMantelTests.test_strict ________________________ self = def test_strict(self): # Matrices have some matching and nonmatching IDs, with different # ordering. x = self.minx_dm_extra.filter(['1', '0', 'foo', '2']) y = self.miny_dm.filter(['0', '2', '1']) z = self.minz_dm_extra.filter(['bar', '1', '2', '0']) np.random.seed(0) # strict=False should discard IDs that aren't found in both matrices obs = pwmantel((x, y, z), alternative='greater', strict=False) > assert_data_frame_almost_equal( obs, self.exp_results_reordered_distance_matrices) skbio/stats/distance/tests/test_mantel.py:407: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ left = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.822 3 pearson 999 greater right = statistic p-value n method permutations alternative dm1 dm2 ...989743 1.000 3 pearson 999 greater 1 2 -0.841698 0.822 3 pearson 999 greater rtol = 1e-05 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right, rtol=1e-5): """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal". Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values are considered "almost equal" if they are within a threshold defined by ``assert_frame_equal``. This wrapper uses a number of checks that are turned off by default in ``assert_frame_equal`` in order to perform stricter comparisons (for example, ensuring the index and column types are the same). It also does not consider empty ``pd.DataFrame`` objects equal if they have a different index. Other notes: * Index (row) and column ordering must be the same for objects to be equal. * NaNs (``np.nan``) in the same locations are considered equal. This is a helper function intended to be used in unit tests that need to compare ``pd.DataFrame`` objects. Parameters ---------- left, right : pd.DataFrame ``pd.DataFrame`` objects to compare. Raises ------ AssertionError If `left` and `right` are not "almost equal". See Also -------- pandas.util.testing.assert_frame_equal """ # pass all kwargs to ensure this function has consistent behavior even if # `assert_frame_equal`'s defaults change > pdt.assert_frame_equal(left, right, check_dtype=True, check_index_type=True, check_column_type=True, check_frame_type=True, check_names=True, by_blocks=False, check_exact=False, rtol=rtol) E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 skbio/util/_testing.py:304: AssertionError _____________ SubsampleCountsTests.test_subsample_counts_nonrandom _____________ self = def test_subsample_counts_nonrandom(self): a = np.array([0, 5, 0]) # Subsample same number of items that are in input (without # replacement). npt.assert_equal(subsample_counts(a, 5), a) # Can only choose from one bin. exp = np.array([0, 2, 0]) > npt.assert_equal(subsample_counts(a, 2), exp) skbio/stats/tests/test_subsample.py:38: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/stats/_subsample.py:246: in subsample_counts result = _subsample_counts_without_replacement(counts, n, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'int64_t' but got 'long' skbio/stats/__subsample.pyx:13: ValueError ________ SubsampleCountsTests.test_subsample_counts_without_replacement ________ self = def test_subsample_counts_without_replacement(self): # Selecting 2 counts from the vector 1000 times yields each of the two # possible results at least once each. a = np.array([2, 0, 1]) actual = set() for i in range(1000): > obs = subsample_counts(a, 2) skbio/stats/tests/test_subsample.py:54: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ skbio/stats/_subsample.py:246: in subsample_counts result = _subsample_counts_without_replacement(counts, n, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'int64_t' but got 'long' skbio/stats/__subsample.pyx:13: ValueError ____________________ ISubsampleTests.test_isubsample_simple ____________________ self = def test_isubsample_simple(self): maximum = 10 def bin_f(x): return x['SequenceID'].rsplit('_', 1)[0] # note, the result here is sorted by sequence_id but is in heap order # by the random values associated to each sequence exp = sorted([('a', {'SequenceID': 'a_5', 'Sequence': 'AATTGGCC-a5'}), ('a', {'SequenceID': 'a_1', 'Sequence': 'AATTGGCC-a1'}), ('a', {'SequenceID': 'a_4', 'Sequence': 'AATTGGCC-a4'}), ('a', {'SequenceID': 'a_3', 'Sequence': 'AATTGGCC-a3'}), ('a', {'SequenceID': 'a_2', 'Sequence': 'AATTGGCC-a2'}), ('b', {'SequenceID': 'b_2', 'Sequence': 'AATTGGCC-b2'}), ('b', {'SequenceID': 'b_1', 'Sequence': 'AATTGGCC-b1'}), ('c', {'SequenceID': 'c_3', 'Sequence': 'AATTGGCC-c3'}), ('c', {'SequenceID': 'c_2', 'Sequence': 'AATTGGCC-c2'}), ('c', {'SequenceID': 'c_1', 'Sequence': 'AATTGGCC-c1'})], key=lambda x: x[0]) obs = isubsample(self.mock_sequence_iter(self.sequences), maximum, bin_f=bin_f) > self.assertEqual(sorted(obs, key=lambda x: x[0]), exp) E AssertionError: Lists differ: [('a'[15 chars]: 'a_3', 'Sequence': 'AATTGGCC-a3'}), ('a', {'[499 chars]3'})] != [('a'[15 chars]: 'a_5', 'Sequence': 'AATTGGCC-a5'}), ('a', {'[499 chars]1'})] E E First differing element 0: E ('a', {'SequenceID': 'a_3', 'Sequence': 'AATTGGCC-a3'}) E ('a', {'SequenceID': 'a_5', 'Sequence': 'AATTGGCC-a5'}) E E Diff is 1356 characters long. Set self.maxDiff to None to see it. skbio/stats/tests/test_subsample.py:158: AssertionError ______________ ISubsampleTests.test_per_sample_sequences_complex _______________ self = def test_per_sample_sequences_complex(self): maximum = 2 def bin_f(x): return x['SequenceID'].rsplit('_', 1)[0] exp = sorted([('a', {'SequenceID': 'a_2', 'Sequence': 'AATTGGCC-a2'}), ('a', {'SequenceID': 'a_3', 'Sequence': 'AATTGGCC-a3'}), ('b', {'SequenceID': 'b_2', 'Sequence': 'AATTGGCC-b2'}), ('b', {'SequenceID': 'b_1', 'Sequence': 'AATTGGCC-b1'}), ('c', {'SequenceID': 'c_1', 'Sequence': 'AATTGGCC-c1'}), ('c', {'SequenceID': 'c_2', 'Sequence': 'AATTGGCC-c2'})], key=lambda x: x[0]) obs = isubsample(self.mock_sequence_iter(self.sequences), maximum, bin_f=bin_f, buf_size=1) > self.assertEqual(sorted(obs, key=lambda x: x[0]), exp) E AssertionError: Lists differ: [('a'[15 chars]: 'a_5', 'Sequence': 'AATTGGCC-a5'}), ('a', {'[271 chars]3'})] != [('a'[15 chars]: 'a_2', 'Sequence': 'AATTGGCC-a2'}), ('a', {'[271 chars]2'})] E E First differing element 0: E ('a', {'SequenceID': 'a_5', 'Sequence': 'AATTGGCC-a5'}) E ('a', {'SequenceID': 'a_2', 'Sequence': 'AATTGGCC-a2'}) E E Diff is 1124 characters long. Set self.maxDiff to None to see it. skbio/stats/tests/test_subsample.py:197: AssertionError ______________ ISubsampleTests.test_per_sample_sequences_min_seqs ______________ self = def test_per_sample_sequences_min_seqs(self): maximum = 10 minimum = 3 def bin_f(x): return x['SequenceID'].rsplit('_', 1)[0] # note, the result here is sorted by sequence_id but is in heap order # by the random values associated to each sequence exp = sorted([('a', {'SequenceID': 'a_5', 'Sequence': 'AATTGGCC-a5'}), ('a', {'SequenceID': 'a_1', 'Sequence': 'AATTGGCC-a1'}), ('a', {'SequenceID': 'a_4', 'Sequence': 'AATTGGCC-a4'}), ('a', {'SequenceID': 'a_3', 'Sequence': 'AATTGGCC-a3'}), ('a', {'SequenceID': 'a_2', 'Sequence': 'AATTGGCC-a2'}), ('c', {'SequenceID': 'c_3', 'Sequence': 'AATTGGCC-c3'}), ('c', {'SequenceID': 'c_2', 'Sequence': 'AATTGGCC-c2'}), ('c', {'SequenceID': 'c_1', 'Sequence': 'AATTGGCC-c1'})], key=lambda x: x[0]) obs = isubsample(self.mock_sequence_iter(self.sequences), maximum, minimum, bin_f=bin_f) > self.assertEqual(sorted(obs, key=lambda x: x[0]), exp) E AssertionError: Lists differ: [('a'[15 chars]: 'a_3', 'Sequence': 'AATTGGCC-a3'}), ('a', {'[385 chars]3'})] != [('a'[15 chars]: 'a_5', 'Sequence': 'AATTGGCC-a5'}), ('a', {'[385 chars]1'})] E E First differing element 0: E ('a', {'SequenceID': 'a_3', 'Sequence': 'AATTGGCC-a3'}) E ('a', {'SequenceID': 'a_5', 'Sequence': 'AATTGGCC-a5'}) E E Diff is 1062 characters long. Set self.maxDiff to None to see it. skbio/stats/tests/test_subsample.py:180: AssertionError =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/joblib/backports.py:7 /usr/lib/python3/dist-packages/joblib/backports.py:7: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.version import LooseVersion ../../../../../../usr/lib/python3/dist-packages/sklearn/utils/multiclass.py:13 /usr/lib/python3/dist-packages/sklearn/utils/multiclass.py:13: DeprecationWarning: Please use `spmatrix` from the `scipy.sparse` namespace, the `scipy.sparse.base` namespace is deprecated. from scipy.sparse.base import spmatrix skbio/stats/ordination/tests/test_redundancy_analysis.py:12 /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_redundancy_analysis.py:12: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as pdt .pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis .pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis_empty_selection /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_indexing.py:116: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. indexable = np.asarray(list(indexable)) .pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative /<>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in true_divide gap_freqs /= length .pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/_base.py:793: RuntimeWarning: invalid value encountered in double_scalars return shannon(counts, base=np.e) / np.log(observed_otus(counts)) .pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/_base.py:869: RuntimeWarning: invalid value encountered in true_divide freqs = counts / counts.sum() .pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/_base.py:793: RuntimeWarning: divide by zero encountered in log return shannon(counts, base=np.e) / np.log(observed_otus(counts)) .pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_invalid_input .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_matrix_unequal_lengths /<>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/_util.py:56: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. counts = np.asarray(counts) .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_block.py: 1 warning .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_driver.py: 9 warnings /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading. warnings.warn('%s is deprecated as of scikit-bio version %s, and ' .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549 /usr/lib/python3/dist-packages/sklearn/metrics/pairwise.py:1765: DataConversionWarning: Data was converted to boolean for metric jaccard warnings.warn(msg, DataConversionWarning) .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_vector_invalid_input /usr/lib/python3/dist-packages/numpy/lib/type_check.py:300: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison return imag(x) == 0 .pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/test_fasta.py::SnifferTests::test_positives /<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/registry.py:918: FormatIdentificationWarning: '_fasta_sniffer' has encountered a problem. Please send the following to our issue tracker at https://github.com/biocore/scikit-bio/issues Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/registry.py", line 914, in wrapped_sniffer return sniffer(fh) File "/<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 648, in _fasta_sniffer for _ in zip(range(num_records), parser): File "/<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 868, in _parse_fasta_raw yield data_parser(data_chunks), id_, desc File "/<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 662, in _sniffer_data_parser _parse_quality_scores(chunks) File "/<>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 883, in _parse_quality_scores quality = np.asarray(qual_str.split(), dtype=int) OverflowError: Python int too large to convert to C long warn("'%s' has encountered a problem.\nPlease" .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites warnings.warn('%s is deprecated as of scikit-bio version %s, and ' .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars warnings.warn('%s is deprecated as of scikit-bio version %s, and ' .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definites warnings.warn('%s is deprecated as of scikit-bio version %s, and ' .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/_sequence.py:1819: RuntimeWarning: invalid value encountered in true_divide obs_counts = obs_counts / len(self) .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py:461: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. Sequence(np.array([1, {}, ()])) .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_munge_to_index_array_valid_iterable /<>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py:2214: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. for c in (lambda x: x, list, tuple, lambda x: np.array(tuple(x)), .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4068: PearsonRConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(PearsonRConstantInputWarning()) .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4529: SpearmanRConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(SpearmanRConstantInputWarning()) .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.541846544269625 and the largest is 16.5872013747859. warn( .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395216 and the largest is 20.90315427793891. warn( .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_not_distance_matrix /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in true_divide proportion_explained = eigvals / sum_eigenvalues .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null .pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:3659: F_onewayConstantInputWarning: Each of the input arrays is constant;the F statistic is not defined or infinite warnings.warn(F_onewayConstantInputWarning()) .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780715 and the largest is 2.707792948946925. warn( .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg /<>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_ordination_results.py:285: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations. fig.tight_layout() .pybuild/cpython3_3.10_skbio/build/skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output /<>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will be removed in version 0.1.4. You should now use skbio.g(). warnings.warn('%s is deprecated as of scikit-bio version %s, and ' -- Docs: https://docs.pytest.org/en/stable/warnings.html =========================== short test summary info ============================ FAILED skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_eq_from_different_source FAILED skbio/alignment/tests/test_tabular_msa.py::TestILoc::test_fancy_empty_second_axis FAILED skbio/diversity/alpha/tests/test_base.py::BaseTests::test_michaelis_menten_fit FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_all_observed FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_extra_tips FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_minimal FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_none_observed FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_qiime_tiny_test FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_root_not_observed FAILED skbio/diversity/alpha/tests/test_lladser.py::LladserTests::test_lladser_ci FAILED skbio/diversity/alpha/tests/test_lladser.py::LladserTests::test_lladser_ci_f3 FAILED skbio/diversity/alpha/tests/test_lladser.py::LladserTests::test_lladser_pe FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_extra_tips FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_minimal_trees FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_otus_out_of_order FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_root_not_observed FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_identity FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_non_overlapping FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_symmetry FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_zero_counts FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_extra_tips FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_minimal_trees FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_normalized_root_not_observed FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_otus_out_of_order FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_root_not_observed FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_identity FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_identity_normalized FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_non_overlapping FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_non_overlapping_normalized FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_normalized FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_symmetry FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_symmetry_normalized FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_zero_counts FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_zero_counts_normalized FAILED skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_empty FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_faith_pd FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_input_types FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_invalid_input FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_no_ids FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_observed_otus FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_optimized FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_single_count_vector FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_alt_pairwise_func FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_invalid_input FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_unweighted_unifrac FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_weighted_unifrac FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_weighted_unifrac_normalized FAILED skbio/diversity/tests/test_driver.py::TestPartialBetaDiversity::test_id_pairs_as_iterable FAILED skbio/diversity/tests/test_driver.py::TestPartialBetaDiversity::test_unweighted_unifrac_partial FAILED skbio/diversity/tests/test_driver.py::TestPartialBetaDiversity::test_weighted_unifrac_partial_full FAILED skbio/diversity/tests/test_util.py::ValidationTests::test_vectorize_counts_and_tree FAILED skbio/io/format/tests/test_fasta.py::SnifferTests::test_positives - As... FAILED skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_eq_from_different_source FAILED skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_degap FAILED skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_eq_from_different_source FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_eq_sequences_from_different_sources_compare_equal FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_boolean_vector_has_qual FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_int_has_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_iterable_of_mixed_has_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_numpy_index_has_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_slice_has_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_tuple_of_mixed_with_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_iter_has_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_reversed_has_positional_metadata FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_slice_positional_metadata FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_all_columns_explicit FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_all_columns_implicit FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_different_column_order FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_single_column FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_vegan_example FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_duplicate_dms FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_filepaths_as_input FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_id_lookup FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_many_filepaths_as_input FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_minimal_compatible_input FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_minimal_compatible_input_with_labels FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_na_p_value FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_reordered_distance_matrices FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_strict FAILED skbio/stats/tests/test_subsample.py::SubsampleCountsTests::test_subsample_counts_nonrandom FAILED skbio/stats/tests/test_subsample.py::SubsampleCountsTests::test_subsample_counts_without_replacement FAILED skbio/stats/tests/test_subsample.py::ISubsampleTests::test_isubsample_simple FAILED skbio/stats/tests/test_subsample.py::ISubsampleTests::test_per_sample_sequences_complex FAILED skbio/stats/tests/test_subsample.py::ISubsampleTests::test_per_sample_sequences_min_seqs ===== 89 failed, 2233 passed, 30 skipped, 68 warnings in 197.65s (0:03:17) ===== E: pybuild pybuild:367: test: plugin distutils failed with: exit code=1: cd /<>/.pybuild/cpython3_3.10_skbio/build; python3.10 -m pytest dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 returned exit code 13 make: *** [debian/rules:14: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2022-03-17T10:46:46Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 30848 Build-Time: 247 Distribution: jammy-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 139 Job: python-skbio_0.5.6-6build1.dsc Machine Architecture: arm64 Package: python-skbio Package-Time: 390 Source-Version: 0.5.6-6build1 Space: 30848 Status: attempted Version: 0.5.6-6build1 -------------------------------------------------------------------------------- Finished at 2022-03-17T10:46:46Z Build needed 00:06:30, 30848k disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-23248678 Scanning for processes to kill in build PACKAGEBUILD-23248678