Tue Mar 26 20:58:57 UTC 2024 I: starting to build python-skbio/bullseye/i386 on jenkins on '2024-03-26 20:58' Tue Mar 26 20:58:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/16135/console.log Tue Mar 26 20:58:57 UTC 2024 I: Downloading source for bullseye/python-skbio=0.5.6-4 --2024-03-26 20:58:57-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/python-skbio/python-skbio_0.5.6-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2812 (2.7K) [text/prs.lines.tag] Saving to: ‘python-skbio_0.5.6-4.dsc’ 0K .. 100% 308M=0s 2024-03-26 20:58:57 (308 MB/s) - ‘python-skbio_0.5.6-4.dsc’ saved [2812/2812] Tue Mar 26 20:58:58 UTC 2024 I: python-skbio_0.5.6-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-skbio Binary: python-skbio-doc, python3-skbio Architecture: any all Version: 0.5.6-4 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille , Kevin Murray Homepage: https://github.com/biocore/scikit-bio Standards-Version: 4.5.1 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), 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 f66d8fc18783b5d03795dfea84c4ddad266101e0 10316 python-skbio_0.5.6-4.debian.tar.xz Checksums-Sha256: 69cf88626ff3803625aa65c7f6792f431318bd31f2b4d5c79e9a71cfc29c37ea 8365758 python-skbio_0.5.6.orig.tar.gz 6ff6220f6d05ea9f4a1f3a595a37c2fbec305b53bfef56490b0651be54428f0a 10316 python-skbio_0.5.6-4.debian.tar.xz Files: 60d30db94b933863cf5a81eb6a9bcc9d 8365758 python-skbio_0.5.6.orig.tar.gz 1828ee77b63f601385968b2555d4a3c8 10316 python-skbio_0.5.6-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmAX4ocACgkQPCZ2P2xn 5uJjpw/8CipgMzcCeg0KPEW8dhHdM05szBw/pCJjjgfhCQ7WyncASl3K6/V/jz1q HFAJcW3SNzrDAGWpchdjBWKTG8BfbtnRZG0EU0ATkqP/xjWLJU40S9ylhEv1rJtI 4JJ7j/zOBshQhSDYm/2ZoJ8PIn11ZPFlRboUlsXKX2lg55VNBl0p6Vye1YR7ugu2 cN5ZKJw49OIuJfcJFi8+KFAMiVZ0HMI7uwxiOOHtzeP2E4WSo7sI5do+GMyi8JNf LRrQbXxNbaKERm/1KvT8nQ884xO//S6bJzyKtcbnGsqhz6JQXyk/7jpBMARnJcCv 3eXxumG5hbdt/LPucRya3fkBmgNWi3CaGemLrU/97Thmsc9sr3eaa77rlH8Xsw+a kbLMFJBorLADwS+hmTfnPMwI3At0SOH1awDnAQ1R+L6TAX2AYygc7uh7R8URvrPI MZMw7+MfibrqPN+ljhRxsRqXzjTFyw84eb1Aw/QEJ5eugC8PUvGj/TeuwNyBlMIh ivlrq9ygh6PlQ+awE9UkeKaDO4FAthxbUJ+Pp+YcNqJQWBYBhNWj+c8RzwbdOzq/ 38DWOuvjO8MAOHfYi0F/dGy5gbas1zSu7MxROpyMCHb2a5KthM9VgKIi1i+LZJse EGW+n5qqtgAu2imA81sVvX2tBON08Ui+xlc0ROO+cJtd7OcGxeU= =D6pW -----END PGP SIGNATURE----- Tue Mar 26 20:58:58 UTC 2024 I: Checking whether the package is not for us Tue Mar 26 20:58:58 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Tue Mar 26 20:58:58 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Tue Mar 26 21:02:23 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 28 15:21:59 -12 2025 I: pbuilder-time-stamp: 1745896919 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [python-skbio_0.5.6-4.dsc] I: copying [./python-skbio_0.5.6.orig.tar.gz] I: copying [./python-skbio_0.5.6-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.FQZWHri2/trustedkeys.kbx': General error gpgv: Signature made Sun Jan 31 23:14:15 2021 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-skbio_0.5.6-4.dsc dpkg-source: info: extracting python-skbio in python-skbio-0.5.6 dpkg-source: info: unpacking python-skbio_0.5.6.orig.tar.gz dpkg-source: info: unpacking python-skbio_0.5.6-4.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/34773/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=22 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='e245c993055a4571b39ff7d349424d52' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='34773' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rapkBBUt/pbuilderrc_spuT --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rapkBBUt/b1 --logfile b1/build.log python-skbio_0.5.6-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin total 5772 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Apr 9 08:02 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 598488 Jan 19 2024 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/34773/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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, python3-sphinx, python3-sphinx-bootstrap-theme, python-numpy-doc, python3-doc, python-matplotlib-doc, python-scipy-doc, python-biom-format-doc, python-pandas-doc, python3-lockfile, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19731 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy (>= 1:1.9.2); however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-cachecontrol; however: Package python3-cachecontrol is not installed. pbuilder-satisfydepends-dummy depends on python3-decorator; however: Package python3-decorator is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas (>= 0.19.2); however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy (>= 1.3.3); however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-ipython; however: Package python3-ipython is not installed. pbuilder-satisfydepends-dummy depends on python3-hdmedians (>= 0.14.1); however: Package python3-hdmedians is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-natsort; however: Package python3-natsort is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on sphinx-common; however: Package sphinx-common is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-bootstrap-theme; however: Package python3-sphinx-bootstrap-theme is not installed. pbuilder-satisfydepends-dummy depends on python-numpy-doc; however: Package python-numpy-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-doc; however: Package python3-doc is not installed. pbuilder-satisfydepends-dummy depends on python-matplotlib-doc; however: Package python-matplotlib-doc is not installed. pbuilder-satisfydepends-dummy depends on python-scipy-doc; however: Package python-scipy-doc is not installed. pbuilder-satisfydepends-dummy depends on python-biom-format-doc; however: Package python-biom-format-doc is not installed. pbuilder-satisfydepends-dummy depends on python-pandas-doc; however: Package python-pandas-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-lockfile; however: Package python3-lockfile is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-lyx{a} fonts-mathjax{a} fonts-open-sans{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libpipeline1{a} libpng16-16{a} libprocps8{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsimde-dev{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} procps{a} python-babel-localedata{a} python-biom-format-doc{a} python-matplotlib-data{a} python-matplotlib-doc{a} python-numpy-doc{a} python-pandas-doc{a} python-scipy-doc{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-babel{a} python3-backcall{a} python3-cachecontrol{a} python3-certifi{a} python3-chardet{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-doc{a} python3-docutils{a} python3-hdmedians{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-ipython{a} python3-ipython-genutils{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lockfile{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-msgpack{a} python3-natsort{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-parso{a} python3-pexpect{a} python3-pickleshare{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-prompt-toolkit{a} python3-ptyprocess{a} python3-py{a} python3-pygments{a} python3-pyparsing{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-bootstrap-theme{a} python3-threadpoolctl{a} python3-toml{a} python3-traitlets{a} python3-tz{a} python3-urllib3{a} python3-wcwidth{a} python3-zipp{a} python3.9{a} python3.9-dev{a} python3.9-doc{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} ttf-bitstream-vera{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils lynx psmisc python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-nose python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-simplejson python3-tables python3-tk python3-xlwt wget 0 packages upgraded, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 272 MB of archives. After unpacking 898 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u5 [101 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 sgml-base all 1.30 [15.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2+deb11u2 [110 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libprocps8 i386 2:3.3.17-5 [64.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 procps i386 2:3.3.17-5 [501 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1w-0+deb11u1 [869 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 cython3 i386 0.29.21-3+b1 [1303 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 docutils-common all 0.16+dfsg-4 [129 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 fonts-lyx all 2.3.6-1 [205 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 fonts-open-sans all 1.11-1.1 [574 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3+deb11u1 [147 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1+deb11u1 [111 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2+deb11u5 [149 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1+deb11u1 [430 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u2 [232 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3+deb11u1 [1960 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 liblbfgsb0 i386 3.0+dfsg.3-9 [28.4 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libpython3.9 i386 3.9.2-1 [1715 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libpython3.9-dev i386 3.9.2-1 [3822 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libpython3-dev i386 3.9.2-3 [21.7 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libpython3-all-dev i386 3.9.2-3 [1068 B] Get: 85 http://deb.debian.org/debian bullseye/main i386 libsimde-dev all 0.7.2-4 [259 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libssw0 i386 1.1-13 [27.1 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libssw-dev i386 1.1-13 [30.2 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1+deb11u2 [269 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1+deb11u5 [306 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libwebpdemux2 i386 0.6.1-2.1+deb11u2 [88.2 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libwebpmux3 i386 0.6.1-2.1+deb11u2 [99.0 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 python-biom-format-doc all 2.1.10-1 [65.9 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 python-matplotlib-doc all 3.3.4-1 [125 MB] Get: 100 http://deb.debian.org/debian bullseye/main i386 python-numpy-doc all 1:1.19.5-1 [9097 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 python-pandas-doc all 1.1.5+dfsg-2 [8196 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 python-scipy-doc all 1.6.0-2 [24.1 MB] Get: 103 http://deb.debian.org/debian bullseye/main i386 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 python3-all i386 3.9.2-3 [1060 B] Get: 105 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 python3.9-dev i386 3.9.2-1 [515 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 python3-dev i386 3.9.2-3 [24.8 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 python3-all-dev i386 3.9.2-3 [1068 B] Get: 109 http://deb.debian.org/debian bullseye/main i386 python3-attr all 20.3.0-1 [52.9 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 python3-tz all 2021.1-1 [34.8 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 python3-backcall all 0.2.0-1 [10.7 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 python3-certifi all 2020.6.20-1 [151 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 python3-chardet all 4.0.0-1 [99.0 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 python3-idna all 2.10-1 [37.4 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-2 [17.5 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 python3-msgpack i386 1.0.0-6+b1 [71.7 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 python3-cachecontrol all 0.12.6-1 [16.4 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 python3-cycler all 0.10.0-3 [8084 B] Get: 123 http://deb.debian.org/debian bullseye/main i386 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 python3-decorator all 4.4.2-2 [15.8 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 python3.9-doc all 3.9.2-1 [10.9 MB] Get: 126 http://deb.debian.org/debian bullseye/main i386 python3-doc all 3.9.2-3 [21.6 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 python3-roman all 2.0.0-5 [9064 B] Get: 128 http://deb.debian.org/debian bullseye/main i386 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 129 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 python3-hdmedians i386 0.14.1-1+b2 [99.5 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 python3-imagesize all 1.2.0-2 [5824 B] Get: 132 http://deb.debian.org/debian bullseye/main i386 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 python3-zipp all 1.0.0-3 [6060 B] Get: 134 http://deb.debian.org/debian bullseye/main i386 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 python3-iniconfig all 1.1.1-1 [6308 B] Get: 136 http://deb.debian.org/debian bullseye/main i386 python3-parso all 0.8.1-1 [65.9 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 python3-jedi all 0.18.0-1 [620 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 python3-ptyprocess all 0.7.0-1 [13.6 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 python3-pexpect all 4.8.0-2 [54.9 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 python3-pickleshare all 0.7.5-3 [7604 B] Get: 141 http://deb.debian.org/debian bullseye/main i386 python3-wcwidth all 0.1.9+dfsg1-2 [18.2 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 python3-prompt-toolkit all 3.0.14-1 [258 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 python3-ipython-genutils all 0.2.0-4 [21.4 kB] Get: 145 http://deb.debian.org/debian bullseye/main i386 python3-traitlets all 5.0.5-1 [84.4 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 python3-ipython all 7.20.0-1+deb11u1 [517 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 python3-markupsafe i386 1.1.1-1+b3 [15.3 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 python3-jinja2 all 2.11.3-1 [114 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 python3-joblib all 0.17.0-4+deb11u1 [214 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 python3-kiwisolver i386 1.3.1-1+b1 [58.5 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 python3-lockfile all 1:0.12.2-2.2 [17.3 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 python3-pyparsing all 2.4.7-1 [109 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 python3-pil i386 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 python3-matplotlib i386 3.3.4-1 [4165 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 python3-natsort all 7.1.0-1 [37.5 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 python3-packaging all 20.9-2 [33.5 kB] Get: 157 http://deb.debian.org/debian bullseye/main i386 python3-pandas-lib i386 1.1.5+dfsg-2 [3182 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 python3-pluggy all 0.13.0-6 [22.3 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 python3-py all 1.10.0-1 [94.2 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 python3-toml all 0.10.1-1 [15.9 kB] Get: 162 http://deb.debian.org/debian bullseye/main i386 python3-pytest all 6.0.2-2 [211 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 python3-scipy i386 1.6.0-2 [11.9 MB] Get: 164 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-4 [366 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 python3-sklearn-lib i386 0.23.2-5 [1789 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 python3-threadpoolctl all 2.1.0-1 [15.3 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 python3-sklearn all 0.23.2-5 [1818 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 sphinx-common all 3.4.3-2 [578 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 python3-sphinx all 3.4.3-2 [545 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 python3-sphinx-bootstrap-theme all 0.7.1-1+deb11u1 [427 kB] Fetched 272 MB in 3s (88.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libicu67:i386 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libmagic1:i386 (1:5.39-3+deb11u1) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3+deb11u1) ... Setting up fonts-open-sans (1.11-1.1) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libncurses6:i386 (6.2+20201114-2+deb11u2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libimagequant0:i386 (2.12.2-1.1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2.1+deb11u2) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up sgml-base (1.30) ... Setting up libtiff5:i386 (4.2.0-1+deb11u5) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libwebpmux3:i386 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:i386 (0.11.3-1+deb11u1) ... Setting up mailcap (3.69) ... Setting up libelf1:i386 (0.183-1) ... Setting up libssw0:i386 (1.1-13) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libprocps8:i386 (2:3.3.17-5) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up mime-support (3.66) ... Setting up libssw-dev:i386 (1.1-13) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:i386 (0.6.1-2.1+deb11u2) ... Setting up libreadline8:i386 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up python3.9-doc (3.9.2-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u2) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1+deb11u1) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up python-matplotlib-doc (3.3.4-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up procps (2:3.3.17-5) ... Setting up python3-doc (3.9.2-3) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up liblbfgsb0:i386 (3.0+dfsg.3-9) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python-numpy-doc (1:1.19.5-1) ... Setting up python-pandas-doc (1.1.5+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python-biom-format-doc (2.1.10-1) ... Setting up dh-autoreconf (20) ... Setting up libpython3.9:i386 (3.9.2-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up python-scipy-doc (1.6.0-2) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:i386 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up python3-tz (2021.1-1) ... Setting up python3-natsort (7.1.0-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:i386 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-wcwidth (0.1.9+dfsg1-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-idna (2.10-1) ... Setting up cython3 (0.29.21-3+b1) ... Setting up python3-pickleshare (0.7.5-3) ... Setting up python3-toml (0.10.1-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-msgpack (1.0.0-6+b1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-ptyprocess (0.7.0-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-prompt-toolkit (3.0.14-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-iniconfig (1.1.1-1) ... Setting up python3-attr (20.3.0-1) ... Setting up python3-lockfile (1:0.12.2-2.2) ... Setting up libpython3-dev:i386 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-py (1.10.0-1) ... Setting up python3-backcall (0.2.0-1) ... Setting up python3-joblib (0.17.0-4+deb11u1) ... Setting up python3-parso (0.8.1-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-ipython-genutils (0.2.0-4) ... Setting up python3-alabaster (0.7.8-1.1) ... Setting up python3-threadpoolctl (2.1.0-1) ... Setting up python3-all (3.9.2-3) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up python3-sphinx-bootstrap-theme (0.7.1-1+deb11u1) ... Setting up libpython3-all-dev:i386 (3.9.2-3) ... Setting up python3-pexpect (4.8.0-2) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-hdmedians (0.14.1-1+b2) ... Setting up python3-traitlets (5.0.5-1) ... Setting up python3-cachecontrol (0.12.6-1) ... Setting up python3-all-dev (3.9.2-3) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-importlib-metadata (1.6.0-2) ... Setting up python3-jedi (0.18.0-1) ... Setting up python3-pandas-lib:i386 (1.1.5+dfsg-2) ... Setting up python3-sklearn-lib:i386 (0.23.2-5) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up python3-ipython (7.20.0-1+deb11u1) ... Setting up python3-sklearn (0.23.2-5) ... Setting up python3-pluggy (0.13.0-6) ... Setting up python3-pytest (6.0.2-2) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-skbio-0.5.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-skbio_0.5.6-4_source.changes dpkg-buildpackage: info: source package python-skbio dpkg-buildpackage: info: source version 0.5.6-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-skbio-0.5.6' 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 '/build/reproducible-path/python-skbio-0.5.6' dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/python-skbio-0.5.6' dh_clean find ./skbio -name '*.so' -delete make[1]: Leaving directory '/build/reproducible-path/python-skbio-0.5.6' debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/python-skbio-0.5.6' dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/benchmarks copying benchmarks/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/benchmarks copying benchmarks/benchmarks.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/benchmarks creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio copying skbio/workflow.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio copying skbio/_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio copying skbio/test.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio copying skbio/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util copying skbio/util/_exception.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util copying skbio/util/_testing.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util copying skbio/util/_warning.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util copying skbio/util/_misc.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util copying skbio/util/_decorator.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util copying skbio/util/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/distance.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_nucleotide_mixin.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_genetic_code.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_repr.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_protein.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_sequence.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_dna.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_grammared_sequence.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence copying skbio/sequence/_rna.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/util.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/_fileobject.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/_exception.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/_iosources.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/_warning.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/registry.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io copying skbio/io/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata copying skbio/metadata/_repr.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata copying skbio/metadata/_testing.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata copying skbio/metadata/_mixin.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata copying skbio/metadata/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata copying skbio/metadata/_interval.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats copying skbio/stats/power.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats copying skbio/stats/gradient.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats copying skbio/stats/_misc.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats copying skbio/stats/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats copying skbio/stats/composition.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats copying skbio/stats/_subsample.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment copying skbio/alignment/_pairwise.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment copying skbio/alignment/_repr.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment copying skbio/alignment/_indexing.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment copying skbio/alignment/_tabular_msa.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment copying skbio/alignment/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tests copying skbio/tests/test_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tests copying skbio/tests/test_workflow.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tests copying skbio/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity copying skbio/diversity/_driver.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity copying skbio/diversity/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity copying skbio/diversity/_block.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity copying skbio/diversity/_util.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree copying skbio/tree/_exception.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree copying skbio/tree/_nj.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree copying skbio/tree/_majority_rule.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree copying skbio/tree/_tree.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree copying skbio/tree/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests copying skbio/util/tests/test_decorator.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests copying skbio/util/tests/test_misc.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests copying skbio/util/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests copying skbio/util/tests/test_testing.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_protein.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_sequence.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_grammared_sequence.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_rna.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_nucleotide_sequences.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_distance.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_genetic_code.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests copying skbio/sequence/tests/test_dna.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/clustal.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/fasta.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/ordination.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/newick.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/emptyfile.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/lsmat.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/fastq.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/genbank.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/gff3.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/stockholm.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/blast7.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/qseq.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/_sequence_feature_vocabulary.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/phylip.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/_blast.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/blast6.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format copying skbio/io/format/embl.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests copying skbio/io/tests/test_util.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests copying skbio/io/tests/test_registry.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests copying skbio/io/tests/test_iosources.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests copying skbio/io/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_ordination.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_genbank.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_qseq.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_newick.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_phylip.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_sequence_feature_vocabulary.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_embl.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_emptyfile.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_fasta.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_lsmat.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_clustal.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_blast7.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_stockholm.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_fastq.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_gff3.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests copying skbio/io/format/tests/test_blast6.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/test_intersection.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/test_mixin.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/test_interval.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests copying skbio/metadata/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_redundancy_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_ordination_results.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_principal_coordinate_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_canonical_correspondence_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_utils.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination copying skbio/stats/ordination/_correspondence_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_power.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_subsample.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_gradient.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_misc.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests copying skbio/stats/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests copying skbio/stats/tests/test_composition.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/evolve copying skbio/stats/evolve/_hommola.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/evolve copying skbio/stats/evolve/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/evolve creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/_permanova.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/_bioenv.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/_mantel.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/_anosim.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance copying skbio/stats/distance/_permdisp.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_ordination_results.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_principal_coordinate_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_util.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_correspondence_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_redundancy_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/evolve/tests copying skbio/stats/evolve/tests/test_hommola.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/evolve/tests copying skbio/stats/evolve/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/evolve/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_bioenv.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_permanova.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_mantel.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_anosim.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_permdisp.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/test_tabular_msa.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/test_ssw.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/test_pairwise.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests copying skbio/alignment/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_lib copying skbio/alignment/_lib/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_lib creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/test_block.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/test_driver.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/test_util.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests copying skbio/diversity/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta copying skbio/diversity/beta/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta copying skbio/diversity/beta/_unifrac.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_ace.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_chao1.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_lladser.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_gini.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha copying skbio/diversity/alpha/_faith_pd.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests copying skbio/diversity/beta/tests/test_unifrac.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests copying skbio/diversity/beta/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_chao1.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_lladser.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_base.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_faith_pd.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_gini.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_ace.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree/tests copying skbio/tree/tests/test_tree.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree/tests copying skbio/tree/tests/test_majority_rule.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree/tests copying skbio/tree/tests/__init__.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree/tests copying skbio/tree/tests/test_nj.py -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/tree/tests creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/real_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/example_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/real_file_2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/big5_file.gz -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/example_file.gz -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/big5_file.bz2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/example_file.bz2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data copying skbio/io/tests/data/big5_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_float -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_simple -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_seq_too_long -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_end_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_multi_char -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_blanks_end_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_short_qual.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_lane -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/empty -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_missing_locus_name -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_single_seq_illumina1.3 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_after_10_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_mixed_qual_scores -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_differing_fields -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_legacy_format -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_for_sniffer_2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_tab.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_2_seqs_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_end_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_empty_str -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_single_record -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_max_width_1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_mixed_nans -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_type_in_column -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_multi_seq_illumina1.3 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_prot_seq_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error19 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_qual.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multi_line_tree_with_id -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_no_qual.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_footer -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_multi_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_two_of_each_metadata -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_single_seq_illumina1.8 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_w_beginning_whitespace -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_qual -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_empty_str -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error11 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_tabular_msa_different_type -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example3_scores -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error10 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_bad_missing_directive -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_blank_lines -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_dna_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blank_lines_between_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_rna_seq_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_multi_record -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_between_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_original_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_seq_too_short -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_legacy_format -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_6_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_sanger_no_description -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_as_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_tree_ids -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_double_qual.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_line_within_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multi_line_tree_no_id -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error24 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_6_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_unrecognized_field -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_header_too_short -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_and_blast7_default -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_middle -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_minimal -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_plus.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_del.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_6_ws_lines_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_with_id -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_multi_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_plus -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_space.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_different_padding -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_no_data -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_sanger_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site_constraints -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_end_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_string -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_between_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error22 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_species -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gc_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_original_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_mixed_nans -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_prot_seqs_odd_labels -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_qual.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_none -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_between_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf_with_whitespace -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_single_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_within_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_multi_char -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blanks_end_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_seq_sanger -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_bio_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_original_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_too_many_columns -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_variable_length_ids -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_prot_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_5 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_original_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_zero_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_line_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_long -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_gibberish -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_length_mismatch -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_constructed -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_y -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_w_beginning_whitespace -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_single_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_seq_data -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_single_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_sequence -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_for_sniffer -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_column_types -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_null.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_negative -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_no_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_line_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_unit_sep.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_single_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_in_seq_at_symbol -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error4 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_multi_char -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_metadata_only -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_whitespace_stripping -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_multi_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record_lower -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_feature_level_record -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_long_qual.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_spaces.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_whitespace_only_lines -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_without_id -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_5_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_gc_data_length -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_tile -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_rna_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_none -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gs_with_whitespace -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_double_seq.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error20 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_nuc_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error18 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_bio_seq_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_all_data_types -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_seq.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_seq_lengths -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_multi_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_short -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_blank_lines -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gs_no_whitespace -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error7 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_5_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error13 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_prot_seqs_odd_labels -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_vtab.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_dna -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_6_ws_lines_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_uniprot_record -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error9 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_ws_line_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_header_too_long -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_no_data -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error6 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_8_fields -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error8 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_zero_seq_len -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_as_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error12 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_plus.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_bio_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_single_seq_sanger -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_as_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_number_of_columns -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive_mixed -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_max_width_5 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_sequence_names -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_gr -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error17 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_gr_data_length -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_5_ws_lines_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gs_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_minimal -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_data_type -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_3_seqs_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_multi_line_trees -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_ws_lines_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_end_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_two_chunks -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_sequence -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq_roundtrip -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_gc -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_msa -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_within_qual -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record_upper -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_few_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error21 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error15 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_references -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_empty_str -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_last -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_desc_mismatch -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_multi_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_nonstring_labels -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_illumina1.3_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_whitespace_only_lines -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_multi_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq_roundtrip -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_bad_wrong_columns -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_prot_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_plus -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_nonexistent_gs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_sanger_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error5 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_data_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_feature_level_record_no_FT -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_references -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_as_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_references_mixed -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_tabs.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_many_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gf_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example2_scores -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_10_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_diff_ids.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_species -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error16 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_3 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_blank_lines_between_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_id_mismatch -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_invalid_differing_fields -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_upper -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_illumina.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_6_blanks_start_of_file -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_lower -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_invalid_too_many_columns -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_filter -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_trees -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_extra -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_dna_3_seqs -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gr_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_rna -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_10_fields -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_first -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_single_line -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_x -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_PCoA_site -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error23 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_tabular_msa_different_type -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_escape.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_nonexistent_gr -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_header -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_multi_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_sequence -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_original_sanger.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_reference_items -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_seq.fastq -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error3 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_read -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_reference -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_dna_seq_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_minimal -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_data_only -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_3_seqs_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_rna_seq_non_defaults -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_empty_str -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_rn_tag -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error14 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data copying skbio/io/format/tests/data/whitespace_only -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_w_msg_out -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_real_raw -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_wo_msg_out -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_no_data_out -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_w_msg_raw -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_out -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/gr_wo_msg_raw -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_data_out -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_raw -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_no_data_raw -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/cr_data_raw -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data copying skbio/stats/tests/data/vr_real_out -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/exp_PCoAEigenResults_site -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_constraints_from_vegan.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/varechem.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_propexpl_from_vegan.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_site_scaling1_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_X -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_site_scaling1_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_eigh_ref_3dim -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/L&L_CA_data -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_fsvd_ref_3dim -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_biplot_from_vegan.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_species_scaling1_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_species_scaling1_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_sites_from_vegan.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_12dim -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_species_from_vegan.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/vare_rda_eigvals_from_vegan.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/varespec.csv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_species_scaling2_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_Y -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/exp_PCoAzeros_site -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_biplot_scaling2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_biplot_projected_descriptors -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_skbio -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_biplot_scaling2 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_X -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_site_scaling2_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_site_scaling2_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_species_scaling2_from_vegan -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_biplot_descriptors -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_biplot_scaling1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_Y -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_biplot_scaling1 -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results_different_column_order.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm4.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_exp_results_vegan.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_all_dms.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/df.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/mantel_env_dm_vegan.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/mantel_veg_dm_vegan.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_duplicate_dms.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_df_vegan.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/df_extra_column.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/moving_pictures_dm.tsv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm_reordered.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_dm_dm2.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_dm_vegan.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/moving_pictures_mf.tsv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm3.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm2.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results_single_column.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/weighted_unifrac_dm.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/tree.nwk -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/weighted_normalized_unifrac_dm.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/otu-table.tsv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/README.md -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/unweighted_unifrac_dm.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/data/qiime-191-tt creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/data creating /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/tree.nwk -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/otu-table.tsv -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/README.md -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/faith-pd.txt -> /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/data/qiime-191-tt running build_ext building 'skbio.metadata._intersection' extension creating build creating build/temp.linux-i386-3.9 creating build/temp.linux-i386-3.9/skbio creating build/temp.linux-i386-3.9/skbio/metadata i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -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/python3.9 -c skbio/metadata/_intersection.c -o build/temp.linux-i386-3.9/skbio/metadata/_intersection.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 skbio/metadata/_intersection.c: In function '__Pyx_ParseOptionalKeywords': skbio/metadata/_intersection.c:11013:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11013 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11013:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 11013 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11013:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11013 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11013:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11013 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11013:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 11013 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11013:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11013 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11029:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11029 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11029:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 11029 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11029:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11029 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11029:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11029 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11029:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 11029 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/metadata/_intersection.c:11029:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 11029 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/metadata/_intersection.c:17: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-3.9/skbio/metadata/_intersection.o -o /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/metadata/_intersection.cpython-39-i386-linux-gnu.so building 'skbio.stats.__subsample' extension creating build/temp.linux-i386-3.9/skbio/stats i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -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/python3.9 -c skbio/stats/__subsample.c -o build/temp.linux-i386-3.9/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:1822, 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:617: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ skbio/stats/__subsample.c: In function '__Pyx_ParseOptionalKeywords': skbio/stats/__subsample.c:5377:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5377 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5377:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 5377 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5377:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5377 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5377:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5377 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5377:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 5377 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5377:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5377 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5393:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5393 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5393:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 5393 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5393:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5393 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5393:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5393 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5393:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 5393 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/stats/__subsample.c:5393:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 5393 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/stats/__subsample.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-3.9/skbio/stats/__subsample.o -o /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/__subsample.cpython-39-i386-linux-gnu.so building 'skbio.alignment._ssw_wrapper' extension creating build/temp.linux-i386-3.9/skbio/alignment i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -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/python3.9 -c skbio/alignment/_ssw_wrapper.c -o build/temp.linux-i386-3.9/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:1822, 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:624: /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 " \ | ^~~~~~~ skbio/alignment/_ssw_wrapper.c: In function '__Pyx_ParseOptionalKeywords': skbio/alignment/_ssw_wrapper.c:12453:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12453:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12453:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12453:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12453:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12453:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12469:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12469 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12469:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 12469 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12469:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12469 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12469:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12469 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12469:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 12469 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/alignment/_ssw_wrapper.c:12469:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 12469 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/alignment/_ssw_wrapper.c:29: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-3.9/skbio/alignment/_ssw_wrapper.o -lssw -o /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_ssw_wrapper.cpython-39-i386-linux-gnu.so building 'skbio.diversity._phylogenetic' extension creating build/temp.linux-i386-3.9/skbio/diversity i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-hfHQKB/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -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/python3.9 -c skbio/diversity/_phylogenetic.c -o build/temp.linux-i386-3.9/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:1822, 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:617: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ skbio/diversity/_phylogenetic.c: In function '__Pyx_ParseOptionalKeywords': skbio/diversity/_phylogenetic.c:6462:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6462 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6462:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 6462 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6462:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6462 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6462:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6462 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6462:21: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 6462 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6462:21: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6462 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6478:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6478 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6478:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 6478 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6478:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6478 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6478:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6478 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6478:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations] 6478 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ skbio/diversity/_phylogenetic.c:6478:25: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations] 6478 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : | ^ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from skbio/diversity/_phylogenetic.c:23: /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/reproducible-path/python-skbio-0.5.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-3.9/skbio/diversity/_phylogenetic.o -o /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/_phylogenetic.cpython-39-i386-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/python-skbio-0.5.6' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/python-skbio-0.5.6' dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py running build_ext PYTHONPATH=/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build \ http_proxy='127.0.0.1:9' \ python3 `which sphinx-build` -b html -d doc/build/doctrees doc/source doc/build/html Running Sphinx v3.4.3 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-c6o5jr_7 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:15: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as pdt making output directory... done /build/reproducible-path/python-skbio-0.5.6/doc/source/conf.py:517: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead. app.add_javascript('copybutton.js') /build/reproducible-path/python-skbio-0.5.6/doc/source/conf.py:518: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('style.css') [autosummary] generating autosummary for: alignment.rst, diversity.rst, index.rst, io.rst, metadata.rst, sequence.rst, stats.rst, tree.rst, util.rst, workflow.rst [autosummary] generating autosummary for: /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.StripedSmithWaterman.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.TabularMSA.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.global_pairwise_align.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.global_pairwise_align_nucleotide.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.global_pairwise_align_protein.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.local_pairwise_align.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.local_pairwise_align_nucleotide.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.local_pairwise_align_protein.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.local_pairwise_align_ssw.rst, ..., /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.assert_data_frame_almost_equal.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.assert_ordination_results_equal.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.cardinal_to_ordinal.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.classproperty.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.find_duplicates.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.get_data_path.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.util.safe_md5.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.Workflow.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.method.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.rst [autosummary] generating autosummary for: /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__eq__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__ge__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__getitem__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__gt__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__hash__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__init_subclass__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__le__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__lt__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__ne__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.alignment.AlignmentStructure.__setstate__.rst, ..., /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__call__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__eq__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__ge__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__gt__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__hash__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__init_subclass__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__le__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__lt__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__ne__.rst, /build/reproducible-path/python-skbio-0.5.6/doc/source/generated/skbio.workflow.requires.__str__.rst loading intersphinx inventory from /usr/share/doc/python3.9/html/objects.inv... loading intersphinx inventory from /usr/share/doc/python-numpy-doc/html/objects.inv... loading intersphinx inventory from /usr/share/doc/python-scipy-doc/html/objects.inv... loading intersphinx inventory from /usr/share/doc/python-matplotlib-doc/html/objects.inv... loading intersphinx inventory from /usr/share/doc/python-pandas-doc/html/objects.inv... loading intersphinx inventory from /usr/share/doc/python-biom-format-doc/html/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 13 source files that are out of date updating environment: [new config] 569 added, 0 changed, 0 removed reading sources... 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[100%] workflow /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/__init__.py:docstring of skbio.diversity:173: WARNING: Exception occurred in plotting diversity-1 from /build/reproducible-path/python-skbio-0.5.6/doc/source/diversity.rst: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/matplotlib/sphinxext/plot_directive.py", line 472, in run_code exec(code, ns) File "", line 34, in File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/_driver.py", line 169, in alpha_diversity counts_by_node, branch_lengths = _setup_faith_pd( File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/_faith_pd.py", line 139, in _setup_faith_pd _vectorize_counts_and_tree(counts, otu_ids, tree) File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/_util.py", line 126, in _vectorize_counts_and_tree counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index) File "skbio/diversity/_phylogenetic.pyx", line 184, in skbio.diversity._phylogenetic._nodes_by_counts ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int' /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/__init__.py:docstring of skbio.diversity:307: WARNING: Exception occurred in plotting diversity-2 from /build/reproducible-path/python-skbio-0.5.6/doc/source/diversity.rst: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/matplotlib/sphinxext/plot_directive.py", line 472, in run_code exec(code, ns) File "", line 9, in NameError: name 'wu_pc' is not defined /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/__init__.py:docstring of skbio.diversity:322: WARNING: Exception occurred in plotting diversity-3 from /build/reproducible-path/python-skbio-0.5.6/doc/source/diversity.rst: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/matplotlib/sphinxext/plot_directive.py", line 472, in run_code exec(code, ns) File "", line 11, in NameError: name 'wu_dm' is not defined /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.ace'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.berger_parker_d'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.brillouin_d'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.chao1'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.chao1_ci'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.dominance'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.doubles'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.enspie'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.esty_ci'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.faith_pd'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.fisher_alpha'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.gini_index'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.goods_coverage'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.heip_e'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.kempton_taylor_q'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.lladser_ci'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.lladser_pe'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.margalef'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.mcintosh_d'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.mcintosh_e'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.menhinick'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.michaelis_menten_fit'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.observed_otus'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.osd'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.pielou_e'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.robbins'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.shannon'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.simpson'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.simpson_e'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.singles'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/__init__.py:docstring of skbio.diversity.alpha.rst:13: WARNING: autosummary: stub file not found 'skbio.diversity.alpha.strong'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/__init__.py:docstring of skbio.diversity.beta.rst:14: WARNING: autosummary: stub file not found 'skbio.diversity.beta.unweighted_unifrac'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/__init__.py:docstring of skbio.diversity.beta.rst:14: WARNING: autosummary: stub file not found 'skbio.diversity.beta.weighted_unifrac'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/registry.py:docstring of skbio.io.registry.rst:9: WARNING: autosummary: stub file not found 'skbio.io.registry.IORegistry'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/registry.py:docstring of skbio.io.registry.rst:9: WARNING: autosummary: stub file not found 'skbio.io.registry.Format'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/registry.py:docstring of skbio.io.registry.rst:18: WARNING: autosummary: stub file not found 'skbio.io.registry.create_format'. Check your autosummary_generate setting. /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/registry.py:docstring of skbio.io.registry.rst:26: WARNING: autosummary: stub file not found 'skbio.io.registry.DuplicateRegistrationError'. 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The HTML pages are in doc/build/html. make[1]: Leaving directory '/build/reproducible-path/python-skbio-0.5.6' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/python-skbio-0.5.6' echo No testing for the -doc package No testing for the -doc package make[1]: Leaving directory '/build/reproducible-path/python-skbio-0.5.6' dh_auto_test -O--buildsystem=pybuild -Npython-skbio-doc I: pybuild base:232: cd /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build; python3.9 -m pytest ============================= test session starts ============================== platform linux -- Python 3.9.2, pytest-6.0.2, py-1.10.0, pluggy-0.13.0 rootdir: /build/reproducible-path/python-skbio-0.5.6 collected 2352 items skbio/alignment/tests/test_pairwise.py ......................... [ 1%] skbio/alignment/tests/test_ssw.py ........................... [ 2%] skbio/alignment/tests/test_tabular_msa.py .............................. 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[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:1659: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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) # array of empty vector actual = alpha_diversity('observed_otus', np.array([[]], dtype=np.int64)) expected = pd.Series([0]) assert_series_almost_equal(actual, expected) # array of empty vectors actual = alpha_diversity('observed_otus', np.array([[], []], dtype=np.int64)) expected = pd.Series([0, 0]) assert_series_almost_equal(actual, expected) # empty vector > actual = alpha_diversity('faith_pd', np.array([], dtype=np.int64), tree=self.tree1, otu_ids=[]) skbio/diversity/tests/test_driver.py:175: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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:126: 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_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:126: 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:126: 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:126: 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_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:126: 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) > actual = alpha_diversity('faith_pd', np.array([1, 3, 0, 1, 0]), tree=self.tree1, otu_ids=self.oids1) skbio/diversity/tests/test_driver.py:199: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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:126: 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_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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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:126: 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 0xee385af0> != .ExamplePositionalMetadataMixin object at 0xee243388> _______________________ 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'): > Sequence(np.int_(50)) E AssertionError: "int64" does not match "Can cannot create a sequence with 'int32'" skbio/sequence/tests/test_sequence.py:477: 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 @experimental(as_of="0.4.0") def assert_data_frame_almost_equal(left, right): """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_less_precise=False, check_names=True, by_blocks=False, check_exact=False) 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 =============================== skbio/util/_testing.py:15 /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:15: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as pdt skbio/sequence/_sequence.py:28 /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:28: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working collections.Sequence, SkbioObject): skbio/io/format/gff3.py:217 /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/gff3.py:217: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working from collections import Iterable skbio/util/_exception.py:10 /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/_exception.py:10: PytestCollectionWarning: cannot collect test class 'TestingUtilError' because it has a __init__ constructor (from: .pybuild/cpython3_3.9_skbio/build/skbio/io/tests/test_registry.py) class TestingUtilError(Exception): skbio/sequence/tests/test_sequence.py:14 /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py:14: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working from collections import Hashable .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_ssw.py: 18 warnings .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py: 5606 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_base.py: 14 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_clustal.py: 57 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_embl.py: 40 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 1632 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 652 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_genbank.py: 34 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_gff3.py: 6 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_phylip.py: 55 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_qseq.py: 108 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_stockholm.py: 58 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/tests/test_registry.py: 6 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_distance.py: 251 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_dna.py: 29 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_genetic_code.py: 1818 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py: 102 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py: 264 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py: 6 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_rna.py: 29 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 1297 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:427: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return self._bytes.tostring() .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_ssw.py: 6 warnings .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py: 3712 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_clustal.py: 18 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 30 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 83 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_phylip.py: 34 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_stockholm.py: 79 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:784: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. self._seqs = pd.Series([]) .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py: 498 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_clustal.py: 1 warning .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 9 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 12 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_phylip.py: 2 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_stockholm.py: 47 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:1991: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. self._seqs = pd.Series(sequences, index=index) .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py: 26 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_blast6.py: 6 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_blast7.py: 8 warnings .pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests/test_mixin.py: 22 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py: 2 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 29 warnings .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py: 3 warnings .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_bioenv.py: 8 warnings .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py: 9 warnings .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py: 21 warnings .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_gradient.py: 4 warnings .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py: 2 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:304: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning. pdt.assert_frame_equal(left, right, .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis_empty_selection .pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_invalid_input .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_matrix_unequal_lengths /usr/lib/python3/dist-packages/numpy/core/_asarray.py:83: 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 return array(a, dtype, copy=False, order=order) .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestExtend::test_non_empty_msa_empty_iterable .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestExtend::test_reset_index_non_empty_msa_empty_iterable /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:1986: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. self._seqs = self._seqs.append(pd.Series(sequences, index=index)) .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py: 62 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_embl.py: 14 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 18 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:1815: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. chars = indices.astype(np.uint8).tostring().decode('ascii') .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in true_divide gap_freqs /= length .pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/_base.py:869: RuntimeWarning: invalid value encountered in true_divide freqs = counts / counts.sum() .pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/diversity/tests/test_block.py: 1 warning .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_driver.py: 9 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/diversity/tests/test_driver.py: 5 warnings .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py: 4 warnings .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py: 2 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:322: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning. pdt.assert_series_equal(left, right, .pybuild/cpython3_3.9_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_3.9_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:276: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison return imag(x) == 0 .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py::SnifferTests::test_positives /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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 "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/registry.py", line 914, in wrapped_sniffer return sniffer(fh) File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/fasta.py", line 648, in _fasta_sniffer for _ in zip(range(num_records), parser): File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/fasta.py", line 868, in _parse_fasta_raw yield data_parser(data_chunks), id_, desc File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/fasta.py", line 662, in _sniffer_data_parser _parse_quality_scores(chunks) File "/build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/fasta.py", line 883, in _parse_quality_scores quality = np.asarray(qual_str.split(), dtype=int) File "/usr/lib/python3/dist-packages/numpy/core/_asarray.py", line 83, in asarray return array(a, dtype, copy=False, order=order) OverflowError: Python int too large to convert to C long warn("'%s' has encountered a problem.\nPlease" .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 52 warnings .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 75 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 3 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:1308: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return str(outbytes.tostring().decode('ascii')) .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py: 19 warnings .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 2 warnings /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_grammared_sequence.py:348: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. [str(b.tostring().decode("ascii")) for b in bad] if .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:1819: RuntimeWarning: invalid value encountered in true_divide obs_counts = obs_counts / len(self) .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_munge_to_index_array_valid_iterable /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/_base.py:550: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. i = pd.Series(i, name='i') .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/_base.py:551: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. j = pd.Series(j, name='j') .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DistanceMatrixTests::test_to_series_1x1 /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py:938: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. exp = pd.Series([], index=[]) .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson /usr/lib/python3/dist-packages/scipy/stats/stats.py:3913: PearsonRConstantInputWarning: An input array is constant; the correlation coefficent is not defined. warnings.warn(PearsonRConstantInputWarning()) .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman /usr/lib/python3/dist-packages/scipy/stats/stats.py:4264: SpearmanRConstantInputWarning: An input array is constant; the correlation coefficent is not defined. warnings.warn(SpearmanRConstantInputWarning()) .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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 -13.541846544269614 and the largest is 16.5872013747859. warn( .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_not_distance_matrix /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in true_divide proportion_explained = eigvals / sum_eigenvalues .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal /usr/lib/python3/dist-packages/scipy/stats/stats.py:3709: F_onewayConstantInputWarning: Each of the input arrays is constant;the F statistic is not defined or infinite warnings.warn(F_onewayConstantInputWarning()) .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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 -0.007758325147780765 and the largest is 2.7077929489469237. warn( .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_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 ' .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py::TestAssertSeriesAlmostEqual::test_equal .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py::TestAssertSeriesAlmostEqual::test_not_equal /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py:231: DeprecationWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. pd.Series(), -- 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_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 ==== 87 failed, 2235 passed, 30 skipped, 17090 warnings in 60.25s (0:01:00) ==== E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/python-skbio-0.5.6/.pybuild/cpython3_3.9_skbio/build; python3.9 -m pytest dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 make: *** [debian/rules:13: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/34773 and its subdirectories Tue Mar 26 21:02:24 UTC 2024 W: No second build log, what happened?