python-skbio →
0.5.6-7 →
armhf → 2022-12-30 07:59:09
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| python-skbio 0.5.6-7 (armhf) Fri, 30 Dec 2022 07:24:43 +0000 |
+==============================================================================+
Package: python-skbio
Version: 0.5.6-7
Source Version: 0.5.6-7
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-d6322d2c-17c6-4a19-a565-6dd1d09f7178' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/python-skbio-YboXsg/resolver-niLPz5' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 11s (2540 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-skbio' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-skbio.git
Please use:
git clone https://salsa.debian.org/med-team/python-skbio.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8386 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main python-skbio 0.5.6-7 (dsc) [2186 B]
Get:2 http://172.17.4.1/private bookworm-staging/main python-skbio 0.5.6-7 (tar) [8366 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main python-skbio 0.5.6-7 (diff) [17.6 kB]
Fetched 8386 kB in 1s (7785 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-skbio-YboXsg/python-skbio-0.5.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-skbio-YboXsg' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cython3, dh-python, python3-all-dev, python3-setuptools, python3-numpy (>= 1:1.9.2), python3-matplotlib, python3-cachecontrol, python3-decorator, python3-pandas (>= 0.19.2), python3-scipy (>= 1.3.3), python3-ipython, python3-hdmedians (>= 0.14.1), python3-sklearn, python3-natsort, libssw-dev, sphinx-common, libsimde-dev, build-essential, fakeroot, python3-lockfile, python3-pytest
Filtered Build-Depends: debhelper-compat (= 13), cython3, dh-python, python3-all-dev, python3-setuptools, python3-numpy (>= 1:1.9.2), python3-matplotlib, python3-cachecontrol, python3-decorator, python3-pandas (>= 0.19.2), python3-scipy (>= 1.3.3), python3-ipython, python3-hdmedians (>= 0.14.1), python3-sklearn, python3-natsort, libssw-dev, sphinx-common, libsimde-dev, build-essential, fakeroot, python3-lockfile, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [534 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [606 B]
Fetched 2103 B in 0s (56.4 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev blt bsdextrautils ca-certificates
cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
fontconfig-config fonts-dejavu-core fonts-lyx gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0
libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72
libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
liblcms2-2 liblerc4 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenjp2-7
libpipeline1 libpng16-16 libproc2-0 libpython3-all-dev libpython3-dev
libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal
libpython3.10-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libqhull-r8.0 libraqm0 libsimde-dev libssw-dev libssw0
libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0
libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1
libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 m4 man-db
media-types openssl po-debconf procps python-matplotlib-data python3
python3-all python3-all-dev python3-appdirs python3-asttokens python3-attr
python3-backcall python3-brotli python3-cachecontrol python3-certifi
python3-chardet python3-charset-normalizer python3-cycler python3-dateutil
python3-decorator python3-dev python3-distutils python3-executing
python3-fonttools python3-fs python3-hdmedians python3-idna
python3-iniconfig python3-ipython python3-jedi python3-joblib
python3-kiwisolver python3-lib2to3 python3-lockfile python3-lxml python3-lz4
python3-matplotlib python3-matplotlib-inline python3-minimal
python3-more-itertools python3-mpmath python3-msgpack python3-natsort
python3-numpy python3-packaging python3-pandas python3-pandas-lib
python3-parso python3-pexpect python3-pickleshare python3-pil
python3-pil.imagetk python3-pkg-resources python3-pluggy
python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-py
python3-pygments python3-pyparsing python3-pytest python3-requests
python3-scipy python3-setuptools python3-six python3-sklearn
python3-sklearn-lib python3-stack-data python3-sympy python3-threadpoolctl
python3-tk python3-tomli python3-traitlets python3-tz python3-ufolib2
python3-unicodedata2 python3-urllib3 python3-wcwidth python3.10
python3.10-dev python3.10-minimal python3.11 python3.11-dev
python3.11-minimal sphinx-common tk8.6-blt2.5 ucf unicode-data x11-common
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc blt-demo cython-doc dh-make flit
python3-build python3-installer gettext-doc libasprintf-dev libgettextpo-dev
groff low-memory-monitor libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python3-doc python3-venv python-attr-doc
python-cycler-doc python-ipython-doc python-lockfile-doc python-lxml-doc
cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0
inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi
python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip
python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc
python3-gmpy2 python-natsort-doc gfortran python-numpy-doc python-pandas-doc
python3-statsmodels python-pexpect-doc python-pil-doc subversion
python-pygments-doc ttf-bitstream-vera python-pyparsing-doc
python3-cryptography python3-openssl python3-socks python-requests-doc
python-scipy-doc python-setuptools-doc python3-dap python-sklearn-doc
texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.10-venv
python3.10-doc binfmt-support python3.11-venv python3.11-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common libjson-xs-perl libltdl-dev
libmail-sendmail-perl psmisc python3-simplejson python3-psutil python3-bs4
python3-html5lib python3-bottleneck python3-numexpr python3-odf
python3-openpyxl python3-xlwt python3-tables python3-jinja2 python3-olefile
python3-nose isympy-common python3-sphinx
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev blt bsdextrautils ca-certificates
cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
fontconfig-config fonts-dejavu-core fonts-lyx gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0
libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72
libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
liblcms2-2 liblerc4 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenjp2-7
libpipeline1 libpng16-16 libproc2-0 libpython3-all-dev libpython3-dev
libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal
libpython3.10-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libqhull-r8.0 libraqm0 libsimde-dev libssw-dev libssw0
libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0
libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1
libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 m4 man-db
media-types openssl po-debconf procps python-matplotlib-data python3
python3-all python3-all-dev python3-appdirs python3-asttokens python3-attr
python3-backcall python3-brotli python3-cachecontrol python3-certifi
python3-chardet python3-charset-normalizer python3-cycler python3-dateutil
python3-decorator python3-dev python3-distutils python3-executing
python3-fonttools python3-fs python3-hdmedians python3-idna
python3-iniconfig python3-ipython python3-jedi python3-joblib
python3-kiwisolver python3-lib2to3 python3-lockfile python3-lxml python3-lz4
python3-matplotlib python3-matplotlib-inline python3-minimal
python3-more-itertools python3-mpmath python3-msgpack python3-natsort
python3-numpy python3-packaging python3-pandas python3-pandas-lib
python3-parso python3-pexpect python3-pickleshare python3-pil
python3-pil.imagetk python3-pkg-resources python3-pluggy
python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-py
python3-pygments python3-pyparsing python3-pytest python3-requests
python3-scipy python3-setuptools python3-six python3-sklearn
python3-sklearn-lib python3-stack-data python3-sympy python3-threadpoolctl
python3-tk python3-tomli python3-traitlets python3-tz python3-ufolib2
python3-unicodedata2 python3-urllib3 python3-wcwidth python3.10
python3.10-dev python3.10-minimal python3.11 python3.11-dev
python3.11-minimal sbuild-build-depends-main-dummy sphinx-common
tk8.6-blt2.5 ucf unicode-data x11-common zlib1g-dev
0 upgraded, 188 newly installed, 0 to remove and 14 not upgraded.
Need to get 116 MB of archives.
After this operation, 518 MB of additional disk space will be used.
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Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.9-1 [769 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.9-1 [1477 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-3 [25.5 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.9-1 [1597 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.9-1 [509 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-3 [8588 B]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-3 [25.2 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-minimal armhf 3.11.1-1 [797 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf python3.11-minimal armhf 3.11.1-1 [1679 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libproc2-0 armhf 2:4.0.2-3 [53.6 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:4.0.2-3 [679 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.7-1 [1349 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.13+dfsg-1 [906 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
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Get:53 http://172.17.4.1/private bookworm-staging/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1 [477 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf blt armhf 2.5.3+dfsg-4.1 [14.9 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf cython3 armhf 0.29.32-2 [1218 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.3 [81.1 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
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Get:63 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
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Get:68 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.3 [942 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf fonts-lyx all 2.3.6.1-1 [206 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
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Get:86 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-2 [116 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 5.3.0-2 [130 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libjson-perl all 4.10000-1 [87.5 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.3-11 [24.3 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.13.1-1 [125 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.5.0-1 [165 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10 armhf 3.10.9-1 [1462 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-dev armhf 3.10.9-1 [2926 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.10.6-3 [8820 B]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-stdlib armhf 3.11.1-1 [1621 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11 armhf 3.11.1-1 [1669 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-dev armhf 3.11.1-1 [3372 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.10.6-3 [1072 B]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libqhull-r8.0 armhf 2020.2-5 [221 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libraqm0 armhf 0.7.0-4 [9388 B]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libsimde-dev all 0.7.2-6 [259 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libssw0 armhf 1.1-13 [21.0 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libssw-dev armhf 1.1-13 [24.0 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2+b1 [237 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-6 [278 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libwebpdemux2 armhf 1.2.2-2+b1 [95.5 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libwebpmux3 armhf 1.2.2-2+b1 [103 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libxslt1.1 armhf 1.1.35-1 [221 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf python-matplotlib-data all 3.5.2-4 [2725 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf python3.11 armhf 3.11.1-1 [567 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf python3-all armhf 3.10.6-3 [1064 B]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf python3.10-dev armhf 3.10.9-1 [512 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.10.6-3 [26.0 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf python3.11-dev armhf 3.11.1-1 [618 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf python3-all-dev armhf 3.10.6-3 [1076 B]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf python3-appdirs all 1.4.4-3 [13.0 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf python3-asttokens all 2.2.0-1 [19.8 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.2.0-1 [65.4 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf python3-backcall all 0.2.0-4 [12.1 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf python3-brotli armhf 1.0.9-2+b2 [278 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf python3-certifi all 2022.9.24-1 [153 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf python3-idna all 3.3-1 [39.4 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf python3-urllib3 all 1.26.12-1 [117 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1 [278 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf python3-msgpack armhf 1.0.3-2 [62.1 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf python3-cachecontrol all 0.12.12-2 [17.9 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf python3-cycler all 0.11.0-1 [8020 B]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf python3-dateutil all 2.8.2-1 [78.2 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf python3-decorator all 5.1.1-3 [14.9 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf python3-executing all 1.2.0-2 [22.6 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.23.5-2+b1 [5285 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf python3-scipy armhf 1.8.1-14+rpi1 [12.9 MB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf python3-ufolib2 all 0.13.1+dfsg1-1 [32.0 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf python3-mpmath all 1.2.1-2 [418 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf python3-sympy all 1.11.1-1 [4358 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf python3-tz all 2022.7-1 [32.1 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf python3-fs all 2.4.16-2 [95.2 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf python3-lxml armhf 4.9.1-1 [959 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf python3-lz4 armhf 4.0.2+dfsg-1 [23.9 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf python3-unicodedata2 armhf 14.0.0+ds2-1 [298 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf unicode-data all 15.0.0-1 [7984 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf python3-fonttools armhf 4.37.4-1 [983 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf python3-hdmedians armhf 0.14.2-5 [82.7 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf python3-parso all 0.8.3-1 [67.4 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf python3-jedi all 0.18.2-1 [689 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf python3-traitlets all 5.5.0-1 [92.4 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf python3-matplotlib-inline all 0.1.6-2 [8652 B]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf python3-ptyprocess all 0.7.0-5 [14.7 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf python3-pexpect all 4.8.0-4 [52.9 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf python3-pickleshare all 0.7.5-5 [7600 B]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf python3-wcwidth all 0.2.5+dfsg1-1 [21.7 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf python3-prompt-toolkit all 3.0.36-1 [276 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf python3-pygments all 2.13.0+dfsg-1 [767 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf python3-pure-eval all 0.2.2-1 [11.2 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf python3-stack-data all 0.6.2-2 [21.8 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1 [519 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf python3-ipython all 8.5.0-3 [516 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf python3-joblib all 1.2.0-4 [211 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf python3-kiwisolver armhf 1.3.2-1+b1 [52.1 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf python3-lockfile all 1:0.12.2-2.2 [17.3 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf python3-pil armhf 9.2.0-1.1 [427 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf python3-tk armhf 3.10.8-1 [101 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf python3-pil.imagetk armhf 9.2.0-1.1 [71.8 kB]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.9-1 [138 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf python3-matplotlib armhf 3.5.2-4 [6479 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf python3-natsort all 8.0.2-2 [39.0 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf python3-pandas-lib armhf 1.3.5+dfsg-6 [2906 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf python3-pandas all 1.3.5+dfsg-6 [2646 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf python3-py all 1.11.0-1 [89.2 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf python3-tomli all 2.0.1-2 [17.9 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-4 [218 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf python3-sklearn-lib armhf 1.1.2+dfsg-91 [1802 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf python3-sklearn all 1.1.2+dfsg-91 [2040 kB]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf sphinx-common all 5.3.0-2 [652 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up media-types (8.0.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up libsimde-dev (0.7.2-6) ...
Setting up liblcms2-2:armhf (2.13.1-1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libicu72:armhf (72.1-3) ...
Setting up liblerc4:armhf (4.0.0+ds-2) ...
Setting up bsdextrautils (2.38.1-4) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.74.1-2) ...
No schema files found: doing nothing.
Setting up fonts-lyx (2.3.6.1-1) ...
Setting up libdebhelper-perl (13.11.3) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up libdeflate0:armhf (1.14-1) ...
Setting up gettext-base (0.21-10) ...
Setting up m4 (1.4.19-1) ...
Setting up libqhull-r8.0:armhf (2020.2-5) ...
Setting up file (1:5.41-4) ...
Setting up libjbig0:armhf (2.1-6.1) ...
Setting up unicode-data (15.0.0-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.5.0-1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up libx11-data (2:1.8.3-3) ...
Setting up libfribidi0:armhf (1.0.8-2.1) ...
Setting up libimagequant0:armhf (2.17.0-1) ...
Setting up libproc2-0:armhf (2:4.0.2-3) ...
Setting up libpng16-16:armhf (1.6.39-2) ...
Setting up libtcl8.6:armhf (8.6.13+dfsg-1) ...
Setting up autopoint (0.21-10) ...
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Setting up ucf (3.0043) ...
Setting up libgfortran5:armhf (12.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libwebp7:armhf (1.2.2-2+b1) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ...
Setting up libmd0:armhf (1.0.4-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up procps (2:4.0.2-3) ...
Setting up libjson-perl (4.10000-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libopenjp2-7:armhf (2.5.0-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libtiff5:armhf (4.4.0-6) ...
Setting up libpython3.11-minimal:armhf (3.11.1-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up python-matplotlib-data (3.5.2-4) ...
Setting up openssl (3.0.7-1) ...
Setting up libwebpmux3:armhf (1.2.2-2+b1) ...
Setting up libbsd0:armhf (0.11.7-1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libssw0:armhf (1.1-13) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.1) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-2) ...
Setting up python3.11-minimal (3.11.1-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-10) ...
Setting up libssw-dev:armhf (1.1-13) ...
Setting up libtool (2.4.7-5) ...
Setting up fontconfig-config (2.13.1-4.5) ...
Setting up libwebpdemux2:armhf (1.2.2-2+b1) ...
Setting up libpython3.11-stdlib:armhf (3.11.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libpython3.10-stdlib:armhf (3.10.9-1) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libjs-sphinxdoc (5.3.0-2) ...
Setting up dh-strip-nondeterminism (1.13.0-2) ...
Setting up dwz (0.14+20220924-2) ...
Setting up groff-base (1.22.4-9) ...
Setting up libxslt1.1:armhf (1.1.35-1) ...
Setting up libx11-6:armhf (2:1.8.3-3) ...
Setting up libharfbuzz0b:armhf (5.2.0-2+b1) ...
Setting up libpython3-stdlib:armhf (3.10.6-3) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.3-11) ...
Setting up python3.11 (3.11.1-1) ...
Setting up libpython3.10:armhf (3.10.9-1) ...
Setting up python3.10 (3.10.9-1) ...
Setting up libpython3.11:armhf (3.11.1-1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up python3 (3.10.6-3) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3-tz (2022.7-1) ...
Setting up python3-natsort (8.0.2-2) ...
Setting up python3-six (1.16.0-4) ...
Setting up python3-decorator (5.1.1-3) ...
Setting up python3-wcwidth (0.2.5+dfsg1-1) ...
Setting up python3-pyparsing (3.0.9-1) ...
Setting up python3-certifi (2022.9.24-1) ...
Setting up libpython3.11-dev:armhf (3.11.1-1) ...
Setting up python3-brotli (1.0.9-2+b2) ...
Setting up libraqm0:armhf (0.7.0-4) ...
Setting up sphinx-common (5.3.0-2) ...
Setting up python3-cycler (0.11.0-1) ...
Setting up python3-kiwisolver (1.3.2-1+b1) ...
Setting up python3-idna (3.3-1) ...
Setting up cython3 (0.29.32-2) ...
Setting up libpython3.10-dev:armhf (3.10.9-1) ...
Setting up python3-pickleshare (0.7.5-5) ...
Setting up python3-urllib3 (1.26.12-1) ...
Setting up python3-pluggy (1.0.0+repack-1) ...
Setting up python3.10-dev (3.10.9-1) ...
Setting up python3-lxml:armhf (4.9.1-1) ...
Setting up python3-traitlets (5.5.0-1) ...
Setting up python3-dateutil (2.8.2-1) ...
Setting up python3-msgpack (1.0.3-2) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up python3-mpmath (1.2.1-2) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up python3-appdirs (1.4.4-3) ...
Setting up python3-ptyprocess (0.7.0-5) ...
Setting up python3-pkg-resources (65.5.0-1) ...
Setting up python3-prompt-toolkit (3.0.36-1) ...
Setting up python3-distutils (3.10.8-1) ...
Setting up dh-python (5.20220819+rpi1) ...
Setting up python3-more-itertools (8.10.0-2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.11.1-1) ...
Setting up python3-attr (22.2.0-1) ...
Setting up python3-lockfile (1:0.12.2-2.2) ...
Setting up python3-pure-eval (0.2.2-1) ...
Setting up libpython3-dev:armhf (3.10.6-3) ...
Setting up python3-setuptools (65.5.0-1) ...
Setting up python3-tomli (2.0.1-2) ...
Setting up python3-py (1.11.0-1) ...
Setting up python3-backcall (0.2.0-4) ...
Setting up python3-joblib (1.2.0-4) ...
Setting up python3-parso (0.8.3-1) ...
Setting up python3-lz4 (4.0.2+dfsg-1) ...
Setting up python3-asttokens (2.2.0-1) ...
Setting up python3.11-dev (3.11.1-1) ...
Setting up python3-charset-normalizer (3.0.1-2) ...
Setting up python3-unicodedata2 (14.0.0+ds2-1) ...
Setting up python3-threadpoolctl (3.1.0-1) ...
Setting up python3-all (3.10.6-3) ...
Setting up debhelper (13.11.3) ...
Setting up python3-matplotlib-inline (0.1.6-2) ...
Setting up python3-fs (2.4.16-2) ...
Setting up python3-pygments (2.13.0+dfsg-1) ...
Setting up python3-packaging (21.3-1.1) ...
Setting up python3-chardet (5.1.0+dfsg-2) ...
Setting up python3-executing (1.2.0-2) ...
Setting up libpython3-all-dev:armhf (3.10.6-3) ...
Setting up python3-pexpect (4.8.0-4) ...
Setting up python3-dev (3.10.6-3) ...
Setting up python3-requests (2.28.1+dfsg-1) ...
Setting up python3-numpy (1:1.23.5-2+b1) ...
Setting up python3-hdmedians (0.14.2-5) ...
Setting up python3-cachecontrol (0.12.12-2) ...
Setting up python3-stack-data (0.6.2-2) ...
Setting up python3-all-dev (3.10.6-3) ...
Setting up python3-scipy (1.8.1-14+rpi1) ...
Setting up python3-jedi (0.18.2-1) ...
Setting up python3-pytest (7.1.2-4) ...
Setting up python3-pandas-lib:armhf (1.3.5+dfsg-6) ...
Setting up python3-sklearn-lib:armhf (1.1.2+dfsg-91) ...
Setting up python3-pandas (1.3.5+dfsg-6) ...
Setting up python3-ipython (8.5.0-3) ...
Setting up python3-sklearn (1.1.2+dfsg-91) ...
Setting up python3-fonttools (4.37.4-1) ...
Setting up python3-ufolib2 (0.13.1+dfsg1-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libtk8.6:armhf (8.6.13-1) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up python3-tk:armhf (3.10.8-1) ...
Setting up python3-pil.imagetk:armhf (9.2.0-1.1) ...
Setting up python3-pil:armhf (9.2.0-1.1) ...
Setting up python3-matplotlib (3.5.2-4) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for libc-bin (2.36-6+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2-2 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+rpi1 blt_2.5.3+dfsg-4.1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-10+rpi1 cython3_0.29.32-2 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.40-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 fonts-lyx_2.3.6.1-1 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-10 gettext-base_0.21-10 gnupg_2.2.40-1 gnupg-l10n_2.2.40-1 gnupg-utils_2.2.40-1 gpg_2.2.40-1 gpg-agent_2.2.40-1 gpg-wks-client_2.2.40-1 gpg-wks-server_2.2.40-1 gpgconf_2.2.40-1 gpgsm_2.2.40-1 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-1 libacl1_2.3.1-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libasan8_12.2.0-10+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-10+rpi1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39.50.20221208-5+rpi1 libblas3_3.11.0-2 libblkid1_2.38.1-4 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-6+rpi1 libc-dev-bin_2.36-6+rpi1 libc6_2.36-6+rpi1 libc6-dev_2.36-6+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-10+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libctf-nobfd0_2.39.50.20221208-5+rpi1 libctf0_2.39.50.20221208-5+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.265 libdebhelper-perl_13.11.3 libdeflate0_1.14-1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-2 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1 libgcc-12-dev_12.2.0-10+rpi1 libgcc-s1_12.2.0-10+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-10+rpi1 libglib2.0-0_2.74.1-2 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10+rpi1 libgpg-error0_1.46-1 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20.1-1 libharfbuzz0b_5.2.0-2+b1 libhogweed6_3.8.1-2 libicu72_72.1-3 libidn2-0_2.3.3-1 libimagequant0_2.17.0-1 libisl23_0.25-1 libjansson4_2.14-2 libjbig0_2.1-6.1 libjpeg62-turbo_1:2.1.2-1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_5.3.0-2 libjs-underscore_1.13.4~dfsg+~1.11.4-2 libjson-perl_4.10000-1 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 libksba8_1.6.2-4 liblapack3_3.11.0-2 liblbfgsb0_3.0+dfsg.3-11 liblcms2-2_2.13.1-1 libldap-2.5-0_2.5.13+dfsg-2+rpi1+b1 liblerc4_4.0.0+ds-2 liblz4-1_1.9.4-1+rpi1 liblzma5_5.4.0-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenjp2-7_2.5.0-1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-3 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libproc2-0_2:4.0.2-3 libpython3-all-dev_3.10.6-3 libpython3-dev_3.10.6-3 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python3-attr_22.2.0-1 python3-backcall_0.2.0-4 python3-brotli_1.0.9-2+b2 python3-cachecontrol_0.12.12-2 python3-certifi_2022.9.24-1 python3-chardet_5.1.0+dfsg-2 python3-charset-normalizer_3.0.1-2 python3-cycler_0.11.0-1 python3-dateutil_2.8.2-1 python3-decorator_5.1.1-3 python3-dev_3.10.6-3 python3-distutils_3.10.8-1 python3-executing_1.2.0-2 python3-fonttools_4.37.4-1 python3-fs_2.4.16-2 python3-hdmedians_0.14.2-5 python3-idna_3.3-1 python3-iniconfig_1.1.1-2 python3-ipython_8.5.0-3 python3-jedi_0.18.2-1 python3-joblib_1.2.0-4 python3-kiwisolver_1.3.2-1+b1 python3-lib2to3_3.10.8-1 python3-lockfile_1:0.12.2-2.2 python3-lxml_4.9.1-1 python3-lz4_4.0.2+dfsg-1 python3-matplotlib_3.5.2-4 python3-matplotlib-inline_0.1.6-2 python3-minimal_3.10.6-3 python3-more-itertools_8.10.0-2 python3-mpmath_1.2.1-2 python3-msgpack_1.0.3-2 python3-natsort_8.0.2-2 python3-numpy_1:1.23.5-2+b1 python3-packaging_21.3-1.1 python3-pandas_1.3.5+dfsg-6 python3-pandas-lib_1.3.5+dfsg-6 python3-parso_0.8.3-1 python3-pexpect_4.8.0-4 python3-pickleshare_0.7.5-5 python3-pil_9.2.0-1.1 python3-pil.imagetk_9.2.0-1.1 python3-pkg-resources_65.5.0-1 python3-pluggy_1.0.0+repack-1 python3-prompt-toolkit_3.0.36-1 python3-ptyprocess_0.7.0-5 python3-pure-eval_0.2.2-1 python3-py_1.11.0-1 python3-pygments_2.13.0+dfsg-1 python3-pyparsing_3.0.9-1 python3-pytest_7.1.2-4 python3-requests_2.28.1+dfsg-1 python3-scipy_1.8.1-14+rpi1 python3-setuptools_65.5.0-1 python3-six_1.16.0-4 python3-sklearn_1.1.2+dfsg-91 python3-sklearn-lib_1.1.2+dfsg-91 python3-stack-data_0.6.2-2 python3-sympy_1.11.1-1 python3-threadpoolctl_3.1.0-1 python3-tk_3.10.8-1 python3-tomli_2.0.1-2 python3-traitlets_5.5.0-1 python3-tz_2022.7-1 python3-ufolib2_0.13.1+dfsg1-1 python3-unicodedata2_14.0.0+ds2-1 python3-urllib3_1.26.12-1 python3-wcwidth_0.2.5+dfsg1-1 python3.10_3.10.9-1 python3.10-dev_3.10.9-1 python3.10-minimal_3.10.9-1 python3.11_3.11.1-1 python3.11-dev_3.11.1-1 python3.11-minimal_3.11.1-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sphinx-common_5.3.0-2 sysvinit-utils_3.05-7 tar_1.34+dfsg-1 tk8.6-blt2.5_2.5.3+dfsg-4.1 tzdata_2022f-1 ucf_3.0043 unicode-data_15.0.0-1 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 x11-common_1:7.7+23 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: python-skbio
Binary: python-skbio-doc, python3-skbio
Architecture: any all
Version: 0.5.6-7
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Kevin Murray <kdmfoss@gmail.com>
Homepage: https://github.com/biocore/scikit-bio
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/python-skbio
Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-pytest
Build-Depends: debhelper-compat (= 13), cython3, dh-python, python3-all-dev, python3-setuptools, python3-numpy (>= 1:1.9.2), python3-matplotlib, python3-cachecontrol, python3-decorator, python3-pandas (>= 0.19.2), python3-scipy (>= 1.3.3), python3-ipython, python3-hdmedians (>= 0.14.1), python3-sklearn, python3-natsort, libssw-dev, sphinx-common, libsimde-dev
Build-Depends-Arch: python3-lockfile <!nocheck>, python3-pytest <!nocheck>
Build-Depends-Indep: python3-sphinx <!nodoc>, python3-sphinx-bootstrap-theme <!nodoc>, python-numpy-doc <!nodoc>, python3-doc <!nodoc>, python-matplotlib-doc <!nodoc>, python-scipy-doc <!nodoc>, python-biom-format-doc <!nodoc>, python-pandas-doc <!nodoc>
Package-List:
python-skbio-doc deb doc optional arch=all profile=!nodoc
python3-skbio deb python optional arch=any
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Files:
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.44UIlkjy/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 21 08:44:48 2022 UTC
gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./python-skbio_0.5.6-7.dsc
dpkg-source: info: extracting python-skbio in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-skbio_0.5.6.orig.tar.gz
dpkg-source: info: unpacking python-skbio_0.5.6-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying mathjax-path
dpkg-source: info: applying 0002-use-libsww-as-library-not-embedded-src.patch
dpkg-source: info: applying no_privacy_breach_logo.patch
dpkg-source: info: applying simde
dpkg-source: info: applying soften_test
dpkg-source: info: applying pandas1.1-ordination-fix.patch
dpkg-source: info: applying pandas1.1-valueerror.patch
dpkg-source: info: applying local_inventory
dpkg-source: info: applying sphinx_add_javascript.patch
dpkg-source: info: applying fix-dtype-precision-warnings.patch
dpkg-source: info: applying precision_bug.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=f6531457acff44088f965ef4ced20cd2
JOURNAL_STREAM=8:31902
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-d6322d2c-17c6-4a19-a565-6dd1d09f7178
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c18615
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package python-skbio
dpkg-buildpackage: info: source version 0.5.6-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
find ./skbio -name '*.so' -delete
find ./skbio -name '*.o' -delete
rm -rf doc/build build doc/source/generated
find doc -name *.doctree -delete
rm -rf .pybuild
rm -f scikit_bio.egg-info/PKG-INFO scikit_bio.egg-info/SOURCES.txt scikit_bio.egg-info/dependency_links.txt scikit_bio.egg-info/requires.txt scikit_bio.egg-info/top_level.txt
rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c
dh_auto_configure
I: pybuild base:240: python3.11 setup.py config
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/skbio/alignment/_ssw_wrapper.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/skbio/diversity/_phylogenetic.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/skbio/metadata/_intersection.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/skbio/stats/__subsample.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling skbio/metadata/_intersection.pyx because it changed.
Compiling skbio/stats/__subsample.pyx because it changed.
Compiling skbio/alignment/_ssw_wrapper.pyx because it changed.
Compiling skbio/diversity/_phylogenetic.pyx because it changed.
[1/4] Cythonizing skbio/alignment/_ssw_wrapper.pyx
[2/4] Cythonizing skbio/diversity/_phylogenetic.pyx
[3/4] Cythonizing skbio/metadata/_intersection.pyx
[4/4] Cythonizing skbio/stats/__subsample.pyx
running config
I: pybuild base:240: python3.10 setup.py config
running config
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:240: /usr/bin/python3.11 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/benchmarks
copying benchmarks/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/benchmarks
copying benchmarks/benchmarks.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/benchmarks
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio
copying skbio/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio
copying skbio/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio
copying skbio/test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio
copying skbio/workflow.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment
copying skbio/alignment/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment
copying skbio/alignment/_repr.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment
copying skbio/alignment/_indexing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment
copying skbio/alignment/_pairwise.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment
copying skbio/alignment/_tabular_msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity
copying skbio/diversity/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity
copying skbio/diversity/_block.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity
copying skbio/diversity/_driver.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity
copying skbio/diversity/_util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/_exception.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/_fileobject.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/_iosources.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/_warning.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
copying skbio/io/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata
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copying skbio/stats/distance/tests/data/dm3.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/dm4.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/dm_reordered.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/exp_results.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/exp_results_different_column_order.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/exp_results_single_column.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/mantel_env_dm_vegan.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/mantel_veg_dm_vegan.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/moving_pictures_dm.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/moving_pictures_mf.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_all_dms.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_dm_dm2.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_duplicate_dms.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/L&L_CA_data -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_biplot_descriptors -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_biplot_projected_descriptors -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_12dim -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_eigh_ref_3dim -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_fsvd_ref_3dim -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_skbio -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_X -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_Y -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_biplot_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_biplot_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_site_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_site_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_species_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_species_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_X -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_Y -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_biplot_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_biplot_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_site_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_site_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_species_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_species_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/exp_PCoAEigenResults_site -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/exp_PCoAzeros_site -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_biplot_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_constraints_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_eigvals_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_propexpl_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_sites_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_species_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/varechem.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/varespec.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/data
running build_ext
building 'skbio.metadata._intersection' extension
creating build
creating build/temp.linux-armhf-cpython-311
creating build/temp.linux-armhf-cpython-311/skbio
creating build/temp.linux-armhf-cpython-311/skbio/metadata
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/python3.11 -c skbio/metadata/_intersection.c -o build/temp.linux-armhf-cpython-311/skbio/metadata/_intersection.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/skbio/metadata/_intersection.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/_intersection.cpython-311-arm-linux-gnueabihf.so
building 'skbio.stats.__subsample' extension
creating build/temp.linux-armhf-cpython-311/skbio/stats
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/python3.11 -c skbio/stats/__subsample.c -o build/temp.linux-armhf-cpython-311/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:1948,
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:5,
from skbio/stats/__subsample.c:773:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/skbio/stats/__subsample.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/__subsample.cpython-311-arm-linux-gnueabihf.so
building 'skbio.alignment._ssw_wrapper' extension
creating build/temp.linux-armhf-cpython-311/skbio/alignment
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iskbio/alignment -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c skbio/alignment/_ssw_wrapper.c -o build/temp.linux-armhf-cpython-311/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:1948,
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:5,
from skbio/alignment/_ssw_wrapper.c:779:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/skbio/alignment/_ssw_wrapper.o -L/usr/lib/arm-linux-gnueabihf -lssw -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/_ssw_wrapper.cpython-311-arm-linux-gnueabihf.so
building 'skbio.diversity._phylogenetic' extension
creating build/temp.linux-armhf-cpython-311/skbio/diversity
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/python3.11 -c skbio/diversity/_phylogenetic.c -o build/temp.linux-armhf-cpython-311/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:1948,
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:5,
from skbio/diversity/_phylogenetic.c:773:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/skbio/diversity/_phylogenetic.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/_phylogenetic.cpython-311-arm-linux-gnueabihf.so
I: pybuild base:240: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/benchmarks
copying benchmarks/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/benchmarks
copying benchmarks/benchmarks.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/benchmarks
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio
copying skbio/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio
copying skbio/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio
copying skbio/test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio
copying skbio/workflow.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment
copying skbio/alignment/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment
copying skbio/alignment/_repr.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment
copying skbio/alignment/_indexing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment
copying skbio/alignment/_pairwise.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment
copying skbio/alignment/_tabular_msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity
copying skbio/diversity/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity
copying skbio/diversity/_block.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity
copying skbio/diversity/_driver.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity
copying skbio/diversity/_util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/_exception.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/_fileobject.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/_iosources.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/_warning.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
copying skbio/io/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata
copying skbio/metadata/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata
copying skbio/metadata/_interval.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata
copying skbio/metadata/_mixin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata
copying skbio/metadata/_repr.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata
copying skbio/metadata/_testing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_dna.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_genetic_code.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_nucleotide_mixin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_protein.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_repr.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_rna.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/distance.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_grammared_sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
copying skbio/sequence/_sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats
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copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data
copying skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/L&L_CA_data -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_biplot_descriptors -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_biplot_projected_descriptors -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_12dim -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_eigh_ref_3dim -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_sample_data_3_fsvd_ref_3dim -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/PCoA_skbio -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_X -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_Y -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_biplot_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_biplot_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_site_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_site_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_species_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example2_species_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_X -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_Y -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_biplot_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_biplot_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_site_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_site_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_species_scaling1_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/example3_species_scaling2_from_vegan -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/exp_PCoAEigenResults_site -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/exp_PCoAzeros_site -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_biplot_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_constraints_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_eigvals_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_propexpl_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_sites_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/vare_rda_species_from_vegan.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/varechem.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
copying skbio/stats/ordination/tests/data/varespec.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/data
running build_ext
building 'skbio.metadata._intersection' extension
creating build/temp.linux-armhf-cpython-310
creating build/temp.linux-armhf-cpython-310/skbio
creating build/temp.linux-armhf-cpython-310/skbio/metadata
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.10 -c skbio/metadata/_intersection.c -o build/temp.linux-armhf-cpython-310/skbio/metadata/_intersection.o -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/skbio/metadata/_intersection.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/metadata/_intersection.cpython-310-arm-linux-gnueabihf.so
building 'skbio.stats.__subsample' extension
creating build/temp.linux-armhf-cpython-310/skbio/stats
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.10 -c skbio/stats/__subsample.c -o build/temp.linux-armhf-cpython-310/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:1948,
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:5,
from skbio/stats/__subsample.c:773:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/skbio/stats/__subsample.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/__subsample.cpython-310-arm-linux-gnueabihf.so
building 'skbio.alignment._ssw_wrapper' extension
creating build/temp.linux-armhf-cpython-310/skbio/alignment
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iskbio/alignment -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.10 -c skbio/alignment/_ssw_wrapper.c -o build/temp.linux-armhf-cpython-310/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:1948,
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:5,
from skbio/alignment/_ssw_wrapper.c:779:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/skbio/alignment/_ssw_wrapper.o -L/usr/lib/arm-linux-gnueabihf -lssw -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_ssw_wrapper.cpython-310-arm-linux-gnueabihf.so
building 'skbio.diversity._phylogenetic' extension
creating build/temp.linux-armhf-cpython-310/skbio/diversity
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.10 -c skbio/diversity/_phylogenetic.c -o build/temp.linux-armhf-cpython-310/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:1948,
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:5,
from skbio/diversity/_phylogenetic.c:773:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/skbio/diversity/_phylogenetic.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/_phylogenetic.cpython-310-arm-linux-gnueabihf.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; python3.11 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.11.1, pytest-7.1.2, pluggy-1.0.0+repack
rootdir: /<<PKGBUILDDIR>>
collected 0 items / 70 errors
==================================== ERRORS ====================================
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_pairwise.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_pairwise.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:212: in <module>
from .registry import write, read, sniff, create_format, io_registry
skbio/io/registry.py:180: in <module>
from .util import _resolve_file, open_file, open_files, _d as _open_kwargs
skbio/io/util.py:38: in <module>
from skbio.util._decorator import stable
skbio/util/__init__.py:57: in <module>
from ._testing import (get_data_path,
skbio/util/_testing.py:15: in <module>
import pandas.testing as pdt
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_ssw.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_ssw.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_tabular_msa.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_tabular_msa.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_ace.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_ace.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_base.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_base.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_chao1.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_chao1.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_faith_pd.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_faith_pd.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_gini.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_gini.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_lladser.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/alpha/tests/test_lladser.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/beta/tests/test_unifrac.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/beta/tests/test_unifrac.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_block.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_block.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_driver.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_driver.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_util.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_util.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_base.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_base.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_base.py:14: in <module>
from skbio import Sequence, DNA, RNA
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_blast6.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_blast6.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_blast6.py:11: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_blast7.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_blast7.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_blast7.py:11: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_clustal.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_clustal.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_clustal.py:13: in <module>
from skbio import TabularMSA
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_embl.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_embl.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_embl.py:12: in <module>
import skbio.io
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_emptyfile.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_emptyfile.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_emptyfile.py:12: in <module>
from skbio.io.format.emptyfile import _empty_file_sniffer
skbio/io/format/emptyfile.py:30: in <module>
from skbio.io import create_format
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_fasta.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_fasta.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_fasta.py:17: in <module>
from skbio import Sequence, DNA, RNA, Protein, TabularMSA
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_fastq.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_fastq.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_fastq.py:15: in <module>
from skbio import read, write, Sequence, DNA, RNA, Protein, TabularMSA
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_genbank.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_genbank.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_genbank.py:12: in <module>
from skbio import Protein, DNA, RNA, Sequence
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_gff3.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_gff3.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_gff3.py:12: in <module>
from skbio.util import get_data_path
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_lsmat.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_lsmat.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_lsmat.py:12: in <module>
from skbio import DistanceMatrix
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_newick.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_newick.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_newick.py:12: in <module>
from skbio import TreeNode
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_ordination.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_ordination.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_ordination.py:13: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_phylip.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_phylip.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_phylip.py:12: in <module>
from skbio.io import PhylipFormatError
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_qseq.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_qseq.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_qseq.py:11: in <module>
from skbio import Sequence, DNA, RNA, Protein
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_sequence_feature_vocabulary.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_sequence_feature_vocabulary.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_sequence_feature_vocabulary.py:11: in <module>
from skbio.io.format._sequence_feature_vocabulary import (
skbio/io/format/_sequence_feature_vocabulary.py:11: in <module>
from skbio.metadata import IntervalMetadata
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_stockholm.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/format/tests/test_stockholm.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/tests/test_stockholm.py:9: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/tests/test_iosources.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/tests/test_iosources.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/tests/test_registry.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/tests/test_registry.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/io/tests/test_util.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/io/tests/test_util.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_intersection.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_intersection.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_interval.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_interval.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_mixin.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_mixin.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_distance.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_distance.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_dna.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_dna.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_genetic_code.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_genetic_code.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_protein.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_protein.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_rna.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_rna.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_anosim.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_anosim.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_base.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_base.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_bioenv.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_bioenv.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_mantel.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_mantel.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permanova.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permanova.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/evolve/tests/test_hommola.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/evolve/tests/test_hommola.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_correspondence_analysis.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_correspondence_analysis.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_redundancy_analysis.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_redundancy_analysis.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_util.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_util.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_composition.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_composition.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_gradient.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_gradient.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_misc.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_misc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_power.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_power.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_subsample.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_subsample.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/tests/test_base.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/tests/test_base.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/tests/test_workflow.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/tests/test_workflow.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/tree/tests/test_majority_rule.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/tree/tests/test_majority_rule.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/tree/tests/test_nj.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/tree/tests/test_nj.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/tree/tests/test_tree.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/tree/tests/test_tree.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_decorator.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_decorator.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_misc.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_misc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
_ ERROR collecting .pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_testing.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_testing.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/__init__.py:11: in <module>
import skbio.io # noqa
skbio/io/__init__.py:240: in <module>
import_module('skbio.io.format.blast6')
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
skbio/io/format/blast6.py:243: in <module>
import pandas as pd
/usr/lib/python3/dist-packages/pandas/__init__.py:28: in <module>
from pandas.compat import (
/usr/lib/python3/dist-packages/pandas/compat/__init__.py:15: in <module>
from pandas.compat.numpy import (
/usr/lib/python3/dist-packages/pandas/compat/numpy/__init__.py:7: in <module>
from pandas.util.version import Version
/usr/lib/python3/dist-packages/pandas/util/__init__.py:1: in <module>
from pandas.util._decorators import ( # noqa
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly # noqa
/usr/lib/python3/dist-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
E ModuleNotFoundError: No module named 'pandas._libs.interval'
=========================== short test summary info ============================
ERROR skbio/alignment/tests/test_pairwise.py
ERROR skbio/alignment/tests/test_ssw.py
ERROR skbio/alignment/tests/test_tabular_msa.py
ERROR skbio/diversity/alpha/tests/test_ace.py
ERROR skbio/diversity/alpha/tests/test_base.py
ERROR skbio/diversity/alpha/tests/test_chao1.py
ERROR skbio/diversity/alpha/tests/test_faith_pd.py
ERROR skbio/diversity/alpha/tests/test_gini.py
ERROR skbio/diversity/alpha/tests/test_lladser.py
ERROR skbio/diversity/beta/tests/test_unifrac.py
ERROR skbio/diversity/tests/test_block.py
ERROR skbio/diversity/tests/test_driver.py
ERROR skbio/diversity/tests/test_util.py
ERROR skbio/io/format/tests/test_base.py
ERROR skbio/io/format/tests/test_blast6.py
ERROR skbio/io/format/tests/test_blast7.py
ERROR skbio/io/format/tests/test_clustal.py
ERROR skbio/io/format/tests/test_embl.py
ERROR skbio/io/format/tests/test_emptyfile.py
ERROR skbio/io/format/tests/test_fasta.py
ERROR skbio/io/format/tests/test_fastq.py
ERROR skbio/io/format/tests/test_genbank.py
ERROR skbio/io/format/tests/test_gff3.py
ERROR skbio/io/format/tests/test_lsmat.py
ERROR skbio/io/format/tests/test_newick.py
ERROR skbio/io/format/tests/test_ordination.py
ERROR skbio/io/format/tests/test_phylip.py
ERROR skbio/io/format/tests/test_qseq.py
ERROR skbio/io/format/tests/test_sequence_feature_vocabulary.py
ERROR skbio/io/format/tests/test_stockholm.py
ERROR skbio/io/tests/test_iosources.py
ERROR skbio/io/tests/test_registry.py
ERROR skbio/io/tests/test_util.py
ERROR skbio/metadata/tests/test_intersection.py
ERROR skbio/metadata/tests/test_interval.py
ERROR skbio/metadata/tests/test_mixin.py
ERROR skbio/sequence/tests/test_distance.py
ERROR skbio/sequence/tests/test_dna.py
ERROR skbio/sequence/tests/test_genetic_code.py
ERROR skbio/sequence/tests/test_grammared_sequence.py
ERROR skbio/sequence/tests/test_nucleotide_sequences.py
ERROR skbio/sequence/tests/test_protein.py
ERROR skbio/sequence/tests/test_rna.py
ERROR skbio/sequence/tests/test_sequence.py
ERROR skbio/stats/distance/tests/test_anosim.py
ERROR skbio/stats/distance/tests/test_base.py
ERROR skbio/stats/distance/tests/test_bioenv.py
ERROR skbio/stats/distance/tests/test_mantel.py
ERROR skbio/stats/distance/tests/test_permanova.py
ERROR skbio/stats/distance/tests/test_permdisp.py
ERROR skbio/stats/evolve/tests/test_hommola.py
ERROR skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py
ERROR skbio/stats/ordination/tests/test_correspondence_analysis.py
ERROR skbio/stats/ordination/tests/test_ordination_results.py
ERROR skbio/stats/ordination/tests/test_principal_coordinate_analysis.py
ERROR skbio/stats/ordination/tests/test_redundancy_analysis.py
ERROR skbio/stats/ordination/tests/test_util.py
ERROR skbio/stats/tests/test_composition.py
ERROR skbio/stats/tests/test_gradient.py
ERROR skbio/stats/tests/test_misc.py
ERROR skbio/stats/tests/test_power.py
ERROR skbio/stats/tests/test_subsample.py
ERROR skbio/tests/test_base.py
ERROR skbio/tests/test_workflow.py
ERROR skbio/tree/tests/test_majority_rule.py
ERROR skbio/tree/tests/test_nj.py
ERROR skbio/tree/tests/test_tree.py
ERROR skbio/util/tests/test_decorator.py
ERROR skbio/util/tests/test_misc.py
ERROR skbio/util/tests/test_testing.py
!!!!!!!!!!!!!!!!!!! Interrupted: 70 errors during collection !!!!!!!!!!!!!!!!!!!
============================== 70 errors in 7.09s ==============================
E: pybuild pybuild:379: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; python3.11 -m pytest
I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build; python3.10 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.10.9, pytest-7.1.2, pluggy-1.0.0+repack
rootdir: /<<PKGBUILDDIR>>
collected 2352 items
skbio/alignment/tests/test_pairwise.py ......................... [ 1%]
skbio/alignment/tests/test_ssw.py ........................... [ 2%]
skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%]
..............F......................................................... [ 6%]
........................................................................ [ 9%]
................................F....................................... [ 12%]
........................................................................ [ 15%]
........................................................................ [ 18%]
............ [ 19%]
skbio/diversity/alpha/tests/test_ace.py .. [ 19%]
skbio/diversity/alpha/tests/test_base.py ..............F......... [ 20%]
skbio/diversity/alpha/tests/test_chao1.py ... [ 20%]
skbio/diversity/alpha/tests/test_faith_pd.py FFF.FFFF [ 20%]
skbio/diversity/alpha/tests/test_gini.py ... [ 21%]
skbio/diversity/alpha/tests/test_lladser.py ..FF.....F.. [ 21%]
skbio/diversity/beta/tests/test_unifrac.py .FFFFFFF.FFFFFFFF.FFFFF.FFFF [ 22%]
skbio/diversity/tests/test_block.py F.......... [ 23%]
skbio/diversity/tests/test_driver.py FFFF.FFFFF....F...FFF.......F...FF [ 24%]
skbio/diversity/tests/test_util.py .........F [ 25%]
skbio/io/format/tests/test_base.py ................................ [ 26%]
skbio/io/format/tests/test_blast6.py ........... [ 26%]
skbio/io/format/tests/test_blast7.py .............. [ 27%]
skbio/io/format/tests/test_clustal.py ............. [ 28%]
skbio/io/format/tests/test_embl.py ............................... [ 29%]
skbio/io/format/tests/test_emptyfile.py .. [ 29%]
skbio/io/format/tests/test_fasta.py .F.............. [ 30%]
skbio/io/format/tests/test_fastq.py ............... [ 30%]
skbio/io/format/tests/test_genbank.py ..................... [ 31%]
skbio/io/format/tests/test_gff3.py ........................ [ 32%]
skbio/io/format/tests/test_lsmat.py ....... [ 32%]
skbio/io/format/tests/test_newick.py ....... [ 33%]
skbio/io/format/tests/test_ordination.py ..... [ 33%]
skbio/io/format/tests/test_phylip.py ....... [ 33%]
skbio/io/format/tests/test_qseq.py ...... [ 34%]
skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 34%]
skbio/io/format/tests/test_stockholm.py ................................ [ 35%]
........................................... [ 37%]
skbio/io/tests/test_iosources.py .......... [ 37%]
skbio/io/tests/test_registry.py ........................................ [ 39%]
...................................................... [ 41%]
skbio/io/tests/test_util.py .........................................sss [ 43%]
sssssssssssssssssssssssssss............................................. [ 46%]
........................................................................ [ 49%]
................................ [ 51%]
skbio/metadata/tests/test_intersection.py ............... [ 51%]
skbio/metadata/tests/test_interval.py .................................. [ 53%]
..................................... [ 54%]
skbio/metadata/tests/test_mixin.py ..................................... [ 56%]
.......F..................................................... [ 58%]
skbio/sequence/tests/test_distance.py .......................... [ 60%]
skbio/sequence/tests/test_dna.py .... [ 60%]
skbio/sequence/tests/test_genetic_code.py .......................... [ 61%]
skbio/sequence/tests/test_grammared_sequence.py .....F.................. [ 62%]
................... [ 63%]
skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 64%]
....... [ 64%]
skbio/sequence/tests/test_protein.py .......... [ 64%]
skbio/sequence/tests/test_rna.py .... [ 65%]
skbio/sequence/tests/test_sequence.py .................................. [ 66%]
..........F............................................................. [ 69%]
....................F...................F...F..F.F.F...F.........F...... [ 72%]
....F........................................................F...F...... [ 75%]
....... [ 75%]
skbio/stats/distance/tests/test_anosim.py .... [ 76%]
skbio/stats/distance/tests/test_base.py ................................ [ 77%]
............................................................... [ 80%]
skbio/stats/distance/tests/test_bioenv.py FFF.........FF... [ 80%]
skbio/stats/distance/tests/test_mantel.py ................F.FFFFF.FFF... [ 82%]
......... [ 82%]
skbio/stats/distance/tests/test_permanova.py .... [ 82%]
skbio/stats/distance/tests/test_permdisp.py ............ [ 83%]
skbio/stats/evolve/tests/test_hommola.py ............ [ 83%]
skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 83%]
..... [ 83%]
skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 84%]
skbio/stats/ordination/tests/test_ordination_results.py ................ [ 84%]
[ 84%]
skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 85%]
...... [ 85%]
skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 85%]
skbio/stats/ordination/tests/test_util.py ......... [ 86%]
skbio/stats/tests/test_composition.py .................................. [ 87%]
........................ [ 88%]
skbio/stats/tests/test_gradient.py .......................... [ 89%]
skbio/stats/tests/test_misc.py ... [ 89%]
skbio/stats/tests/test_power.py ........................................ [ 91%]
... [ 91%]
skbio/stats/tests/test_subsample.py .F..F.F...FF [ 92%]
skbio/tests/test_base.py ..... [ 92%]
skbio/tests/test_workflow.py ................. [ 92%]
skbio/tree/tests/test_majority_rule.py ...... [ 93%]
skbio/tree/tests/test_nj.py ........... [ 93%]
skbio/tree/tests/test_tree.py .......................................... [ 95%]
................................................. [ 97%]
skbio/util/tests/test_decorator.py ....................... [ 98%]
skbio/util/tests/test_misc.py ................... [ 99%]
skbio/util/tests/test_testing.py ............... [100%]
=================================== FAILURES ===================================
________ TestTabularMSAPositionalMetadata.test_eq_from_different_source ________
self = <skbio.alignment.tests.test_tabular_msa.TestTabularMSAPositionalMetadata testMethod=test_eq_from_different_source>
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 = <skbio.alignment.tests.test_tabular_msa.TestILoc testMethod=test_fancy_empty_second_axis>
def test_fancy_empty_second_axis(self):
a = DNA("ACGT", metadata={0: 0}, positional_metadata={0: [1, 2, 3, 4]})
b = DNA("ACGT", metadata={1: 1}, positional_metadata={1: [1, 2, 3, 4]})
c = DNA("ACGT", metadata={2: 2}, positional_metadata={2: [1, 2, 3, 4]})
msa = TabularMSA([a, b, c], metadata={3: 3},
positional_metadata={3: [1, 2, 3, 4]})
> self.assertEqual(self.get(msa, (Ellipsis, [])),
TabularMSA([a[0:0], b[0:0], c[0:0]],
metadata={3: 3},
positional_metadata={3: np.array(
[], dtype=int)}))
E AssertionError: Tabul[86 chars]: int64>
E Stats:
E sequence count: 3
E posi[30 chars]----- != Tabul[86 chars]: int32>
E Stats:
E sequence count: 3
E posi[30 chars]-----
skbio/alignment/tests/test_tabular_msa.py:1660: AssertionError
_____________________ BaseTests.test_michaelis_menten_fit ______________________
self = <skbio.diversity.alpha.tests.test_base.BaseTests testMethod=test_michaelis_menten_fit>
def test_michaelis_menten_fit(self):
> obs = michaelis_menten_fit([22])
skbio/diversity/alpha/tests/test_base.py:177:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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 <listcomp>
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 = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd>
def test_faith_pd(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# phylogenetic diversity implementation
> actual = faith_pd(self.b1[0], self.oids1, self.t1)
skbio/diversity/alpha/tests/test_faith_pd.py:65:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
___________________ FaithPDTests.test_faith_pd_all_observed ____________________
self = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd_all_observed>
def test_faith_pd_all_observed(self):
> actual = faith_pd([1, 1, 1, 1, 1], self.oids1, self.t1)
skbio/diversity/alpha/tests/test_faith_pd.py:51:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
____________________ FaithPDTests.test_faith_pd_extra_tips _____________________
self = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd_extra_tips>
def test_faith_pd_extra_tips(self):
# results are the same despite presences of unobserved tips in tree
> actual = faith_pd(self.b1[0], self.oids1, self.t1_w_extra_tips)
skbio/diversity/alpha/tests/test_faith_pd.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
______________________ FaithPDTests.test_faith_pd_minimal ______________________
self = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd_minimal>
def test_faith_pd_minimal(self):
# two tips
tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;'))
> actual = faith_pd([1, 0], ['OTU1', 'OTU2'], tree)
skbio/diversity/alpha/tests/test_faith_pd.py:96:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
___________________ FaithPDTests.test_faith_pd_none_observed ___________________
self = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd_none_observed>
def test_faith_pd_none_observed(self):
> actual = faith_pd(np.array([], dtype=int),
np.array([], dtype=int),
self.t1)
skbio/diversity/alpha/tests/test_faith_pd.py:41:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
__________________ FaithPDTests.test_faith_pd_qiime_tiny_test __________________
self = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd_qiime_tiny_test>
def test_faith_pd_qiime_tiny_test(self):
# the following table and tree are derived from the QIIME 1.9.1
# "tiny-test" data
tt_table_fp = get_data_path(
os.path.join('qiime-191-tt', 'otu-table.tsv'), 'data')
tt_tree_fp = get_data_path(
os.path.join('qiime-191-tt', 'tree.nwk'), 'data')
self.q_table = pd.read_csv(tt_table_fp, sep='\t', skiprows=1,
index_col=0)
self.q_tree = TreeNode.read(tt_tree_fp)
expected_fp = get_data_path(
os.path.join('qiime-191-tt', 'faith-pd.txt'), 'data')
expected = pd.read_csv(expected_fp, sep='\t', index_col=0)
for sid in self.q_table.columns:
> actual = faith_pd(self.q_table[sid],
otu_ids=self.q_table.index,
tree=self.q_tree)
skbio/diversity/alpha/tests/test_faith_pd.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________ FaithPDTests.test_faith_pd_root_not_observed _________________
self = <skbio.diversity.alpha.tests.test_faith_pd.FaithPDTests testMethod=test_faith_pd_root_not_observed>
def test_faith_pd_root_not_observed(self):
# expected values computed by hand
tree = TreeNode.read(
StringIO('((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)'
'root;'))
otu_ids = ['OTU%d' % i for i in range(1, 5)]
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered observed
> actual = faith_pd([1, 1, 0, 0], otu_ids, tree)
skbio/diversity/alpha/tests/test_faith_pd.py:129:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________________ LladserTests.test_lladser_ci _________________________
self = <skbio.diversity.alpha.tests.test_lladser.LladserTests testMethod=test_lladser_ci>
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 = <skbio.diversity.alpha.tests.test_lladser.LladserTests testMethod=test_lladser_ci_f3>
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 = <skbio.diversity.alpha.tests.test_lladser.LladserTests testMethod=test_lladser_pe>
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 = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_extra_tips>
def test_unweighted_extra_tips(self):
# UniFrac values are the same despite unobserved tips in the tree
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = unweighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1_w_extra_tips)
skbio/diversity/beta/tests/test_unifrac.py:85:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
__________________ UnifracTests.test_unweighted_minimal_trees __________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_minimal_trees>
def test_unweighted_minimal_trees(self):
# two tips
tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;'))
> actual = unweighted_unifrac([1, 0], [0, 0], ['OTU1', 'OTU2'],
tree)
skbio/diversity/beta/tests/test_unifrac.py:104:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ UnifracTests.test_unweighted_otus_out_of_order ________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_otus_out_of_order>
def test_unweighted_otus_out_of_order(self):
# UniFrac API does not assert the observations are in tip order of the
# input tree
shuffled_ids = self.oids1[:]
shuffled_b1 = self.b1.copy()
shuffled_ids[0], shuffled_ids[-1] = shuffled_ids[-1], shuffled_ids[0]
shuffled_b1[:, [0, -1]] = shuffled_b1[:, [-1, 0]]
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = unweighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:58:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ UnifracTests.test_unweighted_root_not_observed ________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_root_not_observed>
def test_unweighted_root_not_observed(self):
# expected values computed with QIIME 1.9.1 and by hand
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered shared
> actual = unweighted_unifrac([1, 1, 0, 0], [1, 0, 0, 0],
self.oids2, self.t2)
skbio/diversity/beta/tests/test_unifrac.py:120:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_____________________ UnifracTests.test_unweighted_unifrac _____________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_unifrac>
def test_unweighted_unifrac(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# unweighted unifrac implementation
# sample A versus all
> actual = unweighted_unifrac(
self.b1[0], self.b1[1], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:338:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ UnifracTests.test_unweighted_unifrac_identity _________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_unifrac_identity>
def test_unweighted_unifrac_identity(self):
for i in range(len(self.b1)):
> actual = unweighted_unifrac(
self.b1[i], self.b1[i], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:174:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_____________ UnifracTests.test_unweighted_unifrac_non_overlapping _____________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_unifrac_non_overlapping>
def test_unweighted_unifrac_non_overlapping(self):
# these communities only share the root node
> actual = unweighted_unifrac(
self.b1[4], self.b1[5], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:310:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ UnifracTests.test_unweighted_unifrac_symmetry _________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_unifrac_symmetry>
def test_unweighted_unifrac_symmetry(self):
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = unweighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:182:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_______________ UnifracTests.test_unweighted_unifrac_zero_counts _______________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_unweighted_unifrac_zero_counts>
def test_unweighted_unifrac_zero_counts(self):
> actual = unweighted_unifrac(
[1, 1, 1, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:320:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:146: in unweighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
____________________ UnifracTests.test_weighted_extra_tips _____________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_extra_tips>
def test_weighted_extra_tips(self):
# UniFrac values are the same despite unobserved tips in the tree
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = weighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1_w_extra_tips)
skbio/diversity/beta/tests/test_unifrac.py:95:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
___________________ UnifracTests.test_weighted_minimal_trees ___________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_minimal_trees>
def test_weighted_minimal_trees(self):
# two tips
tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;'))
> actual = weighted_unifrac([1, 0], [0, 0], ['OTU1', 'OTU2'], tree)
skbio/diversity/beta/tests/test_unifrac.py:112:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
___________ UnifracTests.test_weighted_normalized_root_not_observed ____________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_normalized_root_not_observed>
def test_weighted_normalized_root_not_observed(self):
# expected values computed by hand, these disagree with QIIME 1.9.1
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered shared
> actual = weighted_unifrac([1, 0, 0, 0], [1, 1, 0, 0],
self.oids2, self.t2, normalized=True)
skbio/diversity/beta/tests/test_unifrac.py:160:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________ UnifracTests.test_weighted_otus_out_of_order _________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_otus_out_of_order>
def test_weighted_otus_out_of_order(self):
# UniFrac API does not assert the observations are in tip order of the
# input tree
shuffled_ids = self.oids1[:]
shuffled_b1 = self.b1.copy()
shuffled_ids[0], shuffled_ids[-1] = shuffled_ids[-1], shuffled_ids[0]
shuffled_b1[:, [0, -1]] = shuffled_b1[:, [-1, 0]]
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = weighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:75:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________ UnifracTests.test_weighted_root_not_observed _________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_root_not_observed>
def test_weighted_root_not_observed(self):
# expected values computed by hand, these disagree with QIIME 1.9.1
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered shared
> actual = weighted_unifrac([1, 0, 0, 0], [1, 1, 0, 0],
self.oids2, self.t2)
skbio/diversity/beta/tests/test_unifrac.py:144:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
______________________ UnifracTests.test_weighted_unifrac ______________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac>
def test_weighted_unifrac(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# weighted unifrac implementation
> actual = weighted_unifrac(
self.b1[0], self.b1[1], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:450:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________ UnifracTests.test_weighted_unifrac_identity __________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_identity>
def test_weighted_unifrac_identity(self):
for i in range(len(self.b1)):
> actual = weighted_unifrac(
self.b1[i], self.b1[i], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:405:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
____________ UnifracTests.test_weighted_unifrac_identity_normalized ____________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_identity_normalized>
def test_weighted_unifrac_identity_normalized(self):
for i in range(len(self.b1)):
> actual = weighted_unifrac(
self.b1[i], self.b1[i], self.oids1, self.t1, normalized=True)
skbio/diversity/beta/tests/test_unifrac.py:517:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
______________ UnifracTests.test_weighted_unifrac_non_overlapping ______________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_non_overlapping>
def test_weighted_unifrac_non_overlapping(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# weighted unifrac implementation
# these communities only share the root node
> actual = weighted_unifrac(
self.b1[4], self.b1[5], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:424:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________ UnifracTests.test_weighted_unifrac_non_overlapping_normalized _________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_non_overlapping_normalized>
def test_weighted_unifrac_non_overlapping_normalized(self):
# these communities only share the root node
> actual = weighted_unifrac(
self.b1[4], self.b1[5], self.oids1, self.t1, normalized=True)
skbio/diversity/beta/tests/test_unifrac.py:535:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ UnifracTests.test_weighted_unifrac_normalized _________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_normalized>
def test_weighted_unifrac_normalized(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# weighted unifrac implementation
> actual = weighted_unifrac(
self.b1[0], self.b1[1], self.oids1, self.t1, normalized=True)
skbio/diversity/beta/tests/test_unifrac.py:568:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________ UnifracTests.test_weighted_unifrac_symmetry __________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_symmetry>
def test_weighted_unifrac_symmetry(self):
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = weighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
____________ UnifracTests.test_weighted_unifrac_symmetry_normalized ____________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_symmetry_normalized>
def test_weighted_unifrac_symmetry_normalized(self):
for i in range(len(self.b1)):
for j in range(len(self.b1)):
> actual = weighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1,
normalized=True)
skbio/diversity/beta/tests/test_unifrac.py:525:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ UnifracTests.test_weighted_unifrac_zero_counts ________________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_zero_counts>
def test_weighted_unifrac_zero_counts(self):
> actual = weighted_unifrac(
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1)
skbio/diversity/beta/tests/test_unifrac.py:430:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
__________ UnifracTests.test_weighted_unifrac_zero_counts_normalized ___________
self = <skbio.diversity.beta.tests.test_unifrac.UnifracTests testMethod=test_weighted_unifrac_zero_counts_normalized>
def test_weighted_unifrac_zero_counts_normalized(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# weighted unifrac implementation
> actual = weighted_unifrac(
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1,
normalized=True)
skbio/diversity/beta/tests/test_unifrac.py:549:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/beta/_unifrac.py:280: in weighted_unifrac
_setup_pairwise_unifrac(u_counts, v_counts, otu_ids, tree, validate,
skbio/diversity/beta/_unifrac.py:315: in _setup_pairwise_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_______________ ParallelBetaDiversity.test_block_beta_diversity ________________
self = <skbio.diversity.tests.test_block.ParallelBetaDiversity testMethod=test_block_beta_diversity>
def test_block_beta_diversity(self):
> exp = beta_diversity('unweighted_unifrac', self.table1, self.sids1,
tree=self.tree1, otu_ids=self.oids1)
skbio/diversity/tests/test_block.py:118:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:354: in beta_diversity
metric, counts_by_node = _setup_multiple_unweighted_unifrac(
skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________________ AlphaDiversityTests.test_empty ________________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_empty>
def test_empty(self):
# empty vector
actual = alpha_diversity('observed_otus', np.array([], dtype=np.int64))
expected = pd.Series([0])
> assert_series_almost_equal(actual, expected)
skbio/diversity/tests/test_driver.py:160:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = 0 0
dtype: int32, right = 0 0
dtype: int64
def assert_series_almost_equal(left, right):
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_series_equal`'s defaults change
> pdt.assert_series_equal(left, right,
check_dtype=True,
check_index_type=True,
check_series_type=True,
check_names=True,
check_exact=False,
check_datetimelike_compat=False,
obj='Series')
E AssertionError: Attributes of Series are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:322: AssertionError
______________________ AlphaDiversityTests.test_faith_pd _______________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_faith_pd>
def test_faith_pd(self):
# calling faith_pd through alpha_diversity gives same results as
# calling it directly
expected = []
for e in self.table1:
> expected.append(faith_pd(e, tree=self.tree1, otu_ids=self.oids1))
skbio/diversity/tests/test_driver.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/alpha/_faith_pd.py:122: in faith_pd
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_____________________ AlphaDiversityTests.test_input_types _____________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_input_types>
def test_input_types(self):
list_result = alpha_diversity('observed_otus', [1, 3, 0, 1, 0])
array_result = alpha_diversity('observed_otus',
np.array([1, 3, 0, 1, 0]))
self.assertAlmostEqual(list_result[0], 3)
assert_series_almost_equal(list_result, array_result)
> list_result = alpha_diversity('faith_pd', [1, 3, 0, 1, 0],
tree=self.tree1, otu_ids=self.oids1)
skbio/diversity/tests/test_driver.py:210:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:169: in alpha_diversity
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
____________________ AlphaDiversityTests.test_invalid_input ____________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_invalid_input>
def test_invalid_input(self):
# number of ids doesn't match the number of samples
self.assertRaises(ValueError, alpha_diversity, 'observed_otus',
self.table1, list('ABC'))
# unknown metric provided
self.assertRaises(ValueError, alpha_diversity, 'not-a-metric',
self.table1)
# 3-D list provided as input
self.assertRaises(ValueError, alpha_diversity, 'observed_otus',
[[[43]]])
# negative counts
self.assertRaises(ValueError, alpha_diversity, 'observed_otus',
[0, 3, -12, 42])
# additional kwargs
self.assertRaises(TypeError, alpha_diversity, 'observed_otus',
[0, 1], not_a_real_kwarg=42.0)
> self.assertRaises(TypeError, alpha_diversity, 'faith_pd',
[0, 1], tree=self.tree1, otu_ids=['OTU1', 'OTU2'],
not_a_real_kwarg=42.0)
skbio/diversity/tests/test_driver.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:169: in alpha_diversity
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_______________________ AlphaDiversityTests.test_no_ids ________________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_no_ids>
def test_no_ids(self):
# expected values hand-calculated
expected = pd.Series([3, 3, 3, 3])
actual = alpha_diversity('observed_otus', self.table1)
> assert_series_almost_equal(actual, expected)
skbio/diversity/tests/test_driver.py:254:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = 0 3
1 3
2 3
3 3
dtype: int32
right = 0 3
1 3
2 3
3 3
dtype: int64
def assert_series_almost_equal(left, right):
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_series_equal`'s defaults change
> pdt.assert_series_equal(left, right,
check_dtype=True,
check_index_type=True,
check_series_type=True,
check_names=True,
check_exact=False,
check_datetimelike_compat=False,
obj='Series')
E AssertionError: Attributes of Series are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:322: AssertionError
____________________ AlphaDiversityTests.test_observed_otus ____________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_observed_otus>
def test_observed_otus(self):
# expected values hand-calculated
expected = pd.Series([3, 3, 3, 3], index=self.sids1)
actual = alpha_diversity('observed_otus', self.table1, self.sids1)
> assert_series_almost_equal(actual, expected)
skbio/diversity/tests/test_driver.py:221:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = A 3
B 3
C 3
D 3
dtype: int32
right = A 3
B 3
C 3
D 3
dtype: int64
def assert_series_almost_equal(left, right):
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_series_equal`'s defaults change
> pdt.assert_series_equal(left, right,
check_dtype=True,
check_index_type=True,
check_series_type=True,
check_names=True,
check_exact=False,
check_datetimelike_compat=False,
obj='Series')
E AssertionError: Attributes of Series are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:322: AssertionError
______________________ AlphaDiversityTests.test_optimized ______________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_optimized>
def test_optimized(self):
# calling optimized faith_pd gives same results as calling unoptimized
# version
> optimized = alpha_diversity('faith_pd', self.table1, tree=self.tree1,
otu_ids=self.oids1)
skbio/diversity/tests/test_driver.py:259:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:169: in alpha_diversity
counts_by_node, branch_lengths = _setup_faith_pd(
skbio/diversity/alpha/_faith_pd.py:139: in _setup_faith_pd
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________ AlphaDiversityTests.test_single_count_vector _________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_single_count_vector>
def test_single_count_vector(self):
actual = alpha_diversity('observed_otus', np.array([1, 0, 2]))
expected = pd.Series([2])
> assert_series_almost_equal(actual, expected)
skbio/diversity/tests/test_driver.py:197:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = 0 2
dtype: int32, right = 0 2
dtype: int64
def assert_series_almost_equal(left, right):
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_series_equal`'s defaults change
> pdt.assert_series_equal(left, right,
check_dtype=True,
check_index_type=True,
check_series_type=True,
check_names=True,
check_exact=False,
check_datetimelike_compat=False,
obj='Series')
E AssertionError: Attributes of Series are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:322: AssertionError
__________________ BetaDiversityTests.test_alt_pairwise_func ___________________
self = <skbio.diversity.tests.test_driver.BetaDiversityTests testMethod=test_alt_pairwise_func>
def test_alt_pairwise_func(self):
# confirm that pairwise_func is actually being used
def not_a_real_pdist(counts, metric):
return [[0.0, 42.0], [42.0, 0.0]]
> dm1 = beta_diversity('unweighted_unifrac', self.table1,
otu_ids=self.oids1, tree=self.tree1,
pairwise_func=not_a_real_pdist)
skbio/diversity/tests/test_driver.py:601:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:354: in beta_diversity
metric, counts_by_node = _setup_multiple_unweighted_unifrac(
skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
____________________ BetaDiversityTests.test_invalid_input _____________________
self = <skbio.diversity.tests.test_driver.BetaDiversityTests testMethod=test_invalid_input>
def test_invalid_input(self):
# number of ids doesn't match the number of samples
error_msg = (r"Number of rows")
with self.assertRaisesRegex(ValueError, error_msg):
beta_diversity(self.table1, list('AB'), 'euclidean')
# unknown metric provided
error_msg = r"not-a-metric"
with self.assertRaisesRegex(ValueError, error_msg):
beta_diversity('not-a-metric', self.table1)
# 3-D list provided as input
error_msg = (r"Only 1-D and 2-D")
with self.assertRaisesRegex(ValueError, error_msg):
beta_diversity('euclidean', [[[43]]])
# negative counts
error_msg = r"negative values."
with self.assertRaisesRegex(ValueError, error_msg):
beta_diversity('euclidean', [[0, 1, 3, 4], [0, 3, -12, 42]])
with self.assertRaisesRegex(ValueError, error_msg):
beta_diversity('euclidean', [[0, 1, 3, -4], [0, 3, 12, 42]])
# additional kwargs
error_msg = r"keyword argument"
with self.assertRaisesRegex(TypeError, error_msg):
beta_diversity('euclidean', [[0, 1, 3], [0, 3, 12]],
not_a_real_kwarg=42.0)
with self.assertRaisesRegex(TypeError, error_msg):
> beta_diversity('unweighted_unifrac', [[0, 1, 3], [0, 3, 12]],
not_a_real_kwarg=42.0, tree=self.tree1,
otu_ids=['O1', 'O2', 'O3'])
skbio/diversity/tests/test_driver.py:323:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:354: in beta_diversity
metric, counts_by_node = _setup_multiple_unweighted_unifrac(
skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
__________________ BetaDiversityTests.test_unweighted_unifrac __________________
self = <skbio.diversity.tests.test_driver.BetaDiversityTests testMethod=test_unweighted_unifrac>
def test_unweighted_unifrac(self):
# TODO: update npt.assert_almost_equal calls to use DistanceMatrix
# near-equality testing when that support is available
# expected values calculated by hand
> dm1 = beta_diversity('unweighted_unifrac', self.table1, self.sids1,
otu_ids=self.oids1, tree=self.tree1)
skbio/diversity/tests/test_driver.py:528:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:354: in beta_diversity
metric, counts_by_node = _setup_multiple_unweighted_unifrac(
skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
___________________ BetaDiversityTests.test_weighted_unifrac ___________________
self = <skbio.diversity.tests.test_driver.BetaDiversityTests testMethod=test_weighted_unifrac>
def test_weighted_unifrac(self):
# TODO: update npt.assert_almost_equal calls to use DistanceMatrix
# near-equality testing when that support is available
# expected values calculated by hand
> dm1 = beta_diversity('weighted_unifrac', self.table1, self.sids1,
otu_ids=self.oids1, tree=self.tree1)
skbio/diversity/tests/test_driver.py:547:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:363: in beta_diversity
metric, counts_by_node = _setup_multiple_weighted_unifrac(
skbio/diversity/beta/_unifrac.py:521: in _setup_multiple_weighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_____________ BetaDiversityTests.test_weighted_unifrac_normalized ______________
self = <skbio.diversity.tests.test_driver.BetaDiversityTests testMethod=test_weighted_unifrac_normalized>
def test_weighted_unifrac_normalized(self):
# TODO: update npt.assert_almost_equal calls to use DistanceMatrix
# near-equality testing when that support is available
# expected values calculated by hand
> dm1 = beta_diversity('weighted_unifrac', self.table1, self.sids1,
otu_ids=self.oids1, tree=self.tree1,
normalized=True)
skbio/diversity/tests/test_driver.py:567:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_driver.py:363: in beta_diversity
metric, counts_by_node = _setup_multiple_weighted_unifrac(
skbio/diversity/beta/_unifrac.py:521: in _setup_multiple_weighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
______________ TestPartialBetaDiversity.test_id_pairs_as_iterable ______________
self = <skbio.diversity.tests.test_driver.TestPartialBetaDiversity testMethod=test_id_pairs_as_iterable>
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:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/decorator.py:232: in fun
return caller(func, *(extras + args), **kw)
skbio/util/_decorator.py:260: in wrapped_f
return func(*args[1:], **kwargs)
skbio/diversity/_driver.py:250: in partial_beta_diversity
metric, counts_by_node = _setup_multiple_unweighted_unifrac(
skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
___________ TestPartialBetaDiversity.test_unweighted_unifrac_partial ___________
self = <skbio.diversity.tests.test_driver.TestPartialBetaDiversity testMethod=test_unweighted_unifrac_partial>
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:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/decorator.py:232: in fun
return caller(func, *(extras + args), **kw)
skbio/util/_decorator.py:260: in wrapped_f
return func(*args[1:], **kwargs)
skbio/diversity/_driver.py:250: in partial_beta_diversity
metric, counts_by_node = _setup_multiple_unweighted_unifrac(
skbio/diversity/beta/_unifrac.py:485: in _setup_multiple_unweighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________ TestPartialBetaDiversity.test_weighted_unifrac_partial_full __________
self = <skbio.diversity.tests.test_driver.TestPartialBetaDiversity testMethod=test_weighted_unifrac_partial_full>
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:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/decorator.py:232: in fun
return caller(func, *(extras + args), **kw)
skbio/util/_decorator.py:260: in wrapped_f
return func(*args[1:], **kwargs)
skbio/diversity/_driver.py:259: in partial_beta_diversity
metric, counts_by_node = _setup_multiple_weighted_unifrac(
skbio/diversity/beta/_unifrac.py:521: in _setup_multiple_weighted_unifrac
_setup_multiple_unifrac(counts, otu_ids, tree, validate)
skbio/diversity/beta/_unifrac.py:452: in _setup_multiple_unifrac
_vectorize_counts_and_tree(counts, otu_ids, tree)
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
________________ ValidationTests.test_vectorize_counts_and_tree ________________
self = <skbio.diversity.tests.test_util.ValidationTests testMethod=test_vectorize_counts_and_tree>
def test_vectorize_counts_and_tree(self):
t = TreeNode.read(io.StringIO("((a:1, b:2)c:3)root;"))
counts = np.array([[0, 1], [1, 5], [10, 1]])
count_array, indexed, branch_lengths = \
> _vectorize_counts_and_tree(counts, np.array(['a', 'b']), t)
skbio/diversity/tests/test_util.py:249:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
skbio/diversity/_util.py:130: in _vectorize_counts_and_tree
counts_by_node = _nodes_by_counts(counts, otu_ids, tree_index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'int'
skbio/diversity/_phylogenetic.pyx:184: ValueError
_________________________ SnifferTests.test_positives __________________________
self = <skbio.io.format.tests.test_fasta.SnifferTests testMethod=test_positives>
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 = <skbio.metadata.tests.test_mixin.TestPositionalMetadataMixin testMethod=test_eq_from_different_source>
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: <skbi[60 chars]p.<locals>.ExamplePositionalMetadataMixin object at 0xacf3bc10> != <skbi[60 chars]p.<locals>.ExamplePositionalMetadataMixin object at 0xaca42b08>
_______________________ TestGrammaredSequence.test_degap _______________________
self = <skbio.sequence.tests.test_grammared_sequence.TestGrammaredSequence testMethod=test_degap>
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 = <skbio.sequence.tests.test_sequence.TestSequencePositionalMetadata testMethod=test_eq_from_different_source>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_eq_sequences_from_different_sources_compare_equal>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_boolean_vector_has_qual>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_int_has_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_iterable_of_mixed_has_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_numpy_index_has_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_slice_has_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_tuple_of_mixed_with_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_init_invalid_sequence>
def test_init_invalid_sequence(self):
# invalid dtype (numpy.ndarray input)
with self.assertRaises(TypeError):
# int64
Sequence(np.array([1, 2, 3]))
with self.assertRaises(TypeError):
# |S21
Sequence(np.array([1, "23", 3]))
with self.assertRaises(TypeError):
# object
Sequence(np.array([1, {}, ()]))
# invalid input type (non-numpy.ndarray input)
with self.assertRaisesRegex(TypeError, r'tuple'):
Sequence(('a', 'b', 'c'))
with self.assertRaisesRegex(TypeError, r'list'):
Sequence(['a', 'b', 'c'])
with self.assertRaisesRegex(TypeError, r'set'):
Sequence({'a', 'b', 'c'})
with self.assertRaisesRegex(TypeError, r'dict'):
Sequence({'a': 42, 'b': 43, 'c': 44})
with self.assertRaisesRegex(TypeError, r'int'):
Sequence(42)
with self.assertRaisesRegex(TypeError, r'float'):
Sequence(4.2)
> with self.assertRaisesRegex(TypeError, r'int64'):
E AssertionError: "int64" does not match "Can cannot create a sequence with 'int32'"
skbio/sequence/tests/test_sequence.py:476: AssertionError
________________ TestSequence.test_iter_has_positional_metadata ________________
self = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_iter_has_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_reversed_has_positional_metadata>
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 = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_slice_positional_metadata>
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 = <skbio.stats.distance.tests.test_bioenv.BIOENVTests testMethod=test_bioenv_all_columns_explicit>
def test_bioenv_all_columns_explicit(self):
# Test with all columns being specified.
obs = bioenv(self.dm, self.df, columns=self.cols)
> assert_data_frame_almost_equal(obs, self.exp_results)
skbio/stats/distance/tests/test_bioenv.py:102:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = size correlation
vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143
TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286
right = size correlation
vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143
TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_________________ BIOENVTests.test_bioenv_all_columns_implicit _________________
self = <skbio.stats.distance.tests.test_bioenv.BIOENVTests testMethod=test_bioenv_all_columns_implicit>
def test_bioenv_all_columns_implicit(self):
# Test with all columns in data frame (implicitly).
obs = bioenv(self.dm, self.df)
> assert_data_frame_almost_equal(obs, self.exp_results)
skbio/stats/distance/tests/test_bioenv.py:92:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = size correlation
vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143
TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286
right = size correlation
vars ...LAY, ELEVATION, SOIL_MOISTU... 10 0.607143
TOT_ORG_CARB, SILT_CLAY, ELEVATION, SOIL_MOISTU... 11 0.539286
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
________________ BIOENVTests.test_bioenv_different_column_order ________________
self = <skbio.stats.distance.tests.test_bioenv.BIOENVTests testMethod=test_bioenv_different_column_order>
def test_bioenv_different_column_order(self):
# Specifying columns in a different order will change the row labels in
# the results data frame as the column subsets will be reordered, but
# the actual results (e.g., correlation coefficients) shouldn't change.
obs = bioenv(self.dm, self.df, columns=self.cols[::-1])
> assert_data_frame_almost_equal(
obs,
self.exp_results_different_column_order)
skbio/stats/distance/tests/test_bioenv.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = size correlation
vars ... PH, ANNUAL_SEASON_PRECPT, ... 10 0.607143
LATITUDE, LONGITUDE, CMIN_RATE, PH, ANNUAL_SEAS... 11 0.539286
right = size correlation
vars ... PH, ANNUAL_SEASON_PRECPT, ... 10 0.607143
LATITUDE, LONGITUDE, CMIN_RATE, PH, ANNUAL_SEAS... 11 0.539286
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
____________________ BIOENVTests.test_bioenv_single_column _____________________
self = <skbio.stats.distance.tests.test_bioenv.BIOENVTests testMethod=test_bioenv_single_column>
def test_bioenv_single_column(self):
obs = bioenv(self.dm, self.df, columns=['PH'])
> assert_data_frame_almost_equal(obs, self.exp_results_single_column)
skbio/stats/distance/tests/test_bioenv.py:112:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = size correlation
vars
PH 1 0.75
right = size correlation
vars
PH 1 0.75
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
____________________ BIOENVTests.test_bioenv_vegan_example _____________________
self = <skbio.stats.distance.tests.test_bioenv.BIOENVTests testMethod=test_bioenv_vegan_example>
def test_bioenv_vegan_example(self):
# The correlation coefficient in the first row of the
# results (rho=0.2516) is different from the correlation coefficient
# computed by vegan (rho=0.2513). This seems to occur due to
# differences in numerical precision when calculating the Euclidean
# distances, which affects the rank calculations in Spearman
# (specifically, dealing with ties). The ranked distances end up being
# slightly different between vegan and our implementation because some
# distances are treated as ties in vegan but treated as distinct values
# in our implementation. This explains the difference in rho values. I
# verified that using Pearson correlation instead of Spearman on the
# same distances yields *very* similar results. Thus, the discrepancy
# seems to stem from differences when computing ranks/ties.
obs = bioenv(self.dm_vegan, self.df_vegan)
> assert_data_frame_almost_equal(obs, self.exp_results_vegan, rtol=1e-3)
skbio/stats/distance/tests/test_bioenv.py:149:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = size correlation
vars
P 1...l 4 0.361875
log(N), P, Ca, pH, Al 5 0.321552
log(N), P, K, Ca, pH, Al 6 0.282181
right = size correlation
vars
P 1...l 4 0.361875
log(N), P, Ca, pH, Al 5 0.321552
log(N), P, K, Ca, pH, Al 6 0.282181
rtol = 0.001
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 0] (column name="size") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
____________________ PairwiseMantelTests.test_duplicate_dms ____________________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_duplicate_dms>
def test_duplicate_dms(self):
obs = pwmantel((self.minx_dm, self.minx_dm, self.minx_dm),
alternative='less')
> assert_data_frame_almost_equal(obs, self.exp_results_duplicate_dms)
skbio/stats/distance/tests/test_mantel.py:376:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ... 1.0 1.0 3 pearson 999 less
1 2 1.0 1.0 3 pearson 999 less
right = statistic p-value n method permutations alternative
dm1 dm2 ... 1.0 1.0 3 pearson 999 less
1 2 1.0 1.0 3 pearson 999 less
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_________________ PairwiseMantelTests.test_filepaths_as_input __________________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_filepaths_as_input>
def test_filepaths_as_input(self):
dms = [
get_data_path('dm.txt'),
get_data_path('dm2.txt'),
]
np.random.seed(0)
obs = pwmantel(dms)
> assert_data_frame_almost_equal(obs, self.exp_results_dm_dm2)
skbio/stats/distance/tests/test_mantel.py:465:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2
0 1 0.702031 0.001 6 pearson 999 two-sided
right = statistic p-value n method permutations alternative
dm1 dm2
0 1 0.702031 0.001 6 pearson 999 two-sided
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
______________________ PairwiseMantelTests.test_id_lookup ______________________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_id_lookup>
def test_id_lookup(self):
# Matrices have mismatched IDs but a lookup is provided.
self.minx_dm_extra.ids = ['a', 'b', 'c', 'foo']
self.minz_dm_extra.ids = ['d', 'e', 'f', 'bar']
lookup = {'a': '0', 'b': '1', 'c': '2', 'foo': 'foo',
'd': '0', 'e': '1', 'f': '2', 'bar': 'bar',
'0': '0', '1': '1', '2': '2'}
x = self.minx_dm_extra.filter(['b', 'a', 'foo', 'c'])
y = self.miny_dm.filter(['0', '2', '1'])
z = self.minz_dm_extra.filter(['bar', 'e', 'f', 'd'])
x_copy = x.copy()
y_copy = y.copy()
z_copy = z.copy()
np.random.seed(0)
obs = pwmantel((x, y, z), alternative='greater', strict=False,
lookup=lookup)
> assert_data_frame_almost_equal(
obs,
self.exp_results_reordered_distance_matrices)
skbio/stats/distance/tests/test_mantel.py:431:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.822 3 pearson 999 greater
right = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.822 3 pearson 999 greater
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_______________ PairwiseMantelTests.test_many_filepaths_as_input _______________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_many_filepaths_as_input>
def test_many_filepaths_as_input(self):
dms = [
get_data_path('dm2.txt'),
get_data_path('dm.txt'),
get_data_path('dm4.txt'),
get_data_path('dm3.txt')
]
np.random.seed(0)
obs = pwmantel(dms)
> assert_data_frame_almost_equal(obs, self.exp_results_all_dms)
skbio/stats/distance/tests/test_mantel.py:477:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ...920688 0.004 6 pearson 999 two-sided
2 3 0.717297 0.003 6 pearson 999 two-sided
right = statistic p-value n method permutations alternative
dm1 dm2 ...920688 0.004 6 pearson 999 two-sided
2 3 0.717297 0.003 6 pearson 999 two-sided
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
______________ PairwiseMantelTests.test_minimal_compatible_input _______________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_minimal_compatible_input>
def test_minimal_compatible_input(self):
# Matrices are already in the correct order and have matching IDs.
np.random.seed(0)
# input as DistanceMatrix instances
obs = pwmantel(self.min_dms, alternative='greater')
> assert_data_frame_almost_equal(obs, self.exp_results_minimal)
skbio/stats/distance/tests/test_mantel.py:355:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.835 3 pearson 999 greater
right = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.835 3 pearson 999 greater
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
________ PairwiseMantelTests.test_minimal_compatible_input_with_labels _________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_minimal_compatible_input_with_labels>
def test_minimal_compatible_input_with_labels(self):
np.random.seed(0)
obs = pwmantel(self.min_dms, alternative='greater',
labels=('minx', 'miny', 'minz'))
> assert_data_frame_almost_equal(
obs,
self.exp_results_minimal_with_labels)
skbio/stats/distance/tests/test_mantel.py:369:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ...9743 1.000 3 pearson 999 greater
miny minz -0.841698 0.835 3 pearson 999 greater
right = statistic p-value n method permutations alternative
dm1 dm2 ...9743 1.000 3 pearson 999 greater
miny minz -0.841698 0.835 3 pearson 999 greater
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_____________________ PairwiseMantelTests.test_na_p_value ______________________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_na_p_value>
def test_na_p_value(self):
obs = pwmantel((self.miny_dm, self.minx_dm), method='spearman',
permutations=0)
> assert_data_frame_almost_equal(obs, self.exp_results_na_p_value)
skbio/stats/distance/tests/test_mantel.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2
0 1 0.5 NaN 3 spearman 0 two-sided
right = statistic p-value n method permutations alternative
dm1 dm2
0 1 0.5 NaN 3 spearman 0 two-sided
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_____________ PairwiseMantelTests.test_reordered_distance_matrices _____________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_reordered_distance_matrices>
def test_reordered_distance_matrices(self):
# Matrices have matching IDs but they all have different ordering.
x = self.minx_dm.filter(['1', '0', '2'])
y = self.miny_dm.filter(['0', '2', '1'])
z = self.minz_dm.filter(['1', '2', '0'])
np.random.seed(0)
obs = pwmantel((x, y, z), alternative='greater')
> assert_data_frame_almost_equal(
obs,
self.exp_results_reordered_distance_matrices)
skbio/stats/distance/tests/test_mantel.py:392:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.822 3 pearson 999 greater
right = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.822 3 pearson 999 greater
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_______________________ PairwiseMantelTests.test_strict ________________________
self = <skbio.stats.distance.tests.test_mantel.PairwiseMantelTests testMethod=test_strict>
def test_strict(self):
# Matrices have some matching and nonmatching IDs, with different
# ordering.
x = self.minx_dm_extra.filter(['1', '0', 'foo', '2'])
y = self.miny_dm.filter(['0', '2', '1'])
z = self.minz_dm_extra.filter(['bar', '1', '2', '0'])
np.random.seed(0)
# strict=False should discard IDs that aren't found in both matrices
obs = pwmantel((x, y, z), alternative='greater', strict=False)
> assert_data_frame_almost_equal(
obs,
self.exp_results_reordered_distance_matrices)
skbio/stats/distance/tests/test_mantel.py:407:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.822 3 pearson 999 greater
right = statistic p-value n method permutations alternative
dm1 dm2 ...989743 1.000 3 pearson 999 greater
1 2 -0.841698 0.822 3 pearson 999 greater
rtol = 1e-05
@experimental(as_of="0.4.0")
def assert_data_frame_almost_equal(left, right, rtol=1e-5):
"""Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".
Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values
are considered "almost equal" if they are within a threshold defined by
``assert_frame_equal``. This wrapper uses a number of
checks that are turned off by default in ``assert_frame_equal`` in order to
perform stricter comparisons (for example, ensuring the index and column
types are the same). It also does not consider empty ``pd.DataFrame``
objects equal if they have a different index.
Other notes:
* Index (row) and column ordering must be the same for objects to be equal.
* NaNs (``np.nan``) in the same locations are considered equal.
This is a helper function intended to be used in unit tests that need to
compare ``pd.DataFrame`` objects.
Parameters
----------
left, right : pd.DataFrame
``pd.DataFrame`` objects to compare.
Raises
------
AssertionError
If `left` and `right` are not "almost equal".
See Also
--------
pandas.util.testing.assert_frame_equal
"""
# pass all kwargs to ensure this function has consistent behavior even if
# `assert_frame_equal`'s defaults change
> pdt.assert_frame_equal(left, right,
check_dtype=True,
check_index_type=True,
check_column_type=True,
check_frame_type=True,
check_names=True,
by_blocks=False,
check_exact=False,
rtol=rtol)
E AssertionError: Attributes of DataFrame.iloc[:, 2] (column name="n") are different
E
E Attribute "dtype" are different
E [left]: int32
E [right]: int64
skbio/util/_testing.py:304: AssertionError
_____________ SubsampleCountsTests.test_subsample_counts_nonrandom _____________
self = <skbio.stats.tests.test_subsample.SubsampleCountsTests testMethod=test_subsample_counts_nonrandom>
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 = <skbio.stats.tests.test_subsample.SubsampleCountsTests testMethod=test_subsample_counts_without_replacement>
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 = <skbio.stats.tests.test_subsample.ISubsampleTests testMethod=test_isubsample_simple>
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 = <skbio.stats.tests.test_subsample.ISubsampleTests testMethod=test_per_sample_sequences_complex>
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 = <skbio.stats.tests.test_subsample.ISubsampleTests testMethod=test_per_sample_sequences_min_seqs>
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/stats/ordination/tests/test_redundancy_analysis.py:12
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_redundancy_analysis.py:12: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
import pandas.util.testing as pdt
.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis
.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis_empty_selection
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_indexing.py:116: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
indexable = np.asarray(list(indexable))
.pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide
gap_freqs /= length
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/_base.py:793: RuntimeWarning: invalid value encountered in double_scalars
return shannon(counts, base=np.e) / np.log(observed_otus(counts))
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/_base.py:869: RuntimeWarning: invalid value encountered in divide
freqs = counts / counts.sum()
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/alpha/_base.py:793: RuntimeWarning: divide by zero encountered in log
return shannon(counts, base=np.e) / np.log(observed_otus(counts))
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_invalid_input
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_matrix_unequal_lengths
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/_util.py:56: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
counts = np.asarray(counts)
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_block.py: 1 warning
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_driver.py: 9 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading.
warnings.warn('%s is deprecated as of scikit-bio version %s, and '
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549
/usr/lib/python3/dist-packages/sklearn/metrics/pairwise.py:2008: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
.pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_vector_invalid_input
/usr/lib/python3/dist-packages/numpy/lib/type_check.py:300: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
return imag(x) == 0
.pybuild/cpython3_3.10_skbio/build/skbio/io/format/tests/test_fasta.py::SnifferTests::test_positives
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io/registry.py:918: FormatIdentificationWarning: '_fasta_sniffer' has encountered a problem.
Please send the following to our issue tracker at
https://github.com/biocore/scikit-bio/issues
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io/registry.py", line 914, in wrapped_sniffer
return sniffer(fh)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 648, in _fasta_sniffer
for _ in zip(range(num_records), parser):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 868, in _parse_fasta_raw
yield data_parser(data_chunks), id_, desc
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 662, in _sniffer_data_parser
_parse_quality_scores(chunks)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/io/format/fasta.py", line 883, in _parse_quality_scores
quality = np.asarray(qual_str.split(), dtype=int)
OverflowError: Python int too large to convert to C long
warn("'%s' has encountered a problem.\nPlease"
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites
warnings.warn('%s is deprecated as of scikit-bio version %s, and '
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars
warnings.warn('%s is deprecated as of scikit-bio version %s, and '
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definites
warnings.warn('%s is deprecated as of scikit-bio version %s, and '
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/_sequence.py:1819: RuntimeWarning: invalid value encountered in divide
obs_counts = obs_counts / len(self)
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py:461: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
Sequence(np.array([1, {}, ()]))
.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_munge_to_index_array_valid_iterable
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py:2214: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
for c in (lambda x: x, list, tuple, lambda x: np.array(tuple(x)),
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
/usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4068: PearsonRConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
warnings.warn(PearsonRConstantInputWarning())
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
/usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4529: SpearmanRConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
warnings.warn(SpearmanRConstantInputWarning())
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.541846544269625 and the largest is 16.5872013747859.
warn(
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395216 and the largest is 20.90315427793891.
warn(
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_not_distance_matrix
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide
proportion_explained = eigvals / sum_eigenvalues
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
.pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
/usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:3659: F_onewayConstantInputWarning: Each of the input arrays is constant;the F statistic is not defined or infinite
warnings.warn(F_onewayConstantInputWarning())
.pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780715 and the largest is 2.707792948946925.
warn(
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg
.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_ordination_results.py:285: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations.
fig.tight_layout()
.pybuild/cpython3_3.10_skbio/build/skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254: DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will be removed in version 0.1.4. You should now use skbio.g().
warnings.warn('%s is deprecated as of scikit-bio version %s, and '
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_eq_from_different_source
FAILED skbio/alignment/tests/test_tabular_msa.py::TestILoc::test_fancy_empty_second_axis
FAILED skbio/diversity/alpha/tests/test_base.py::BaseTests::test_michaelis_menten_fit
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_all_observed
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_extra_tips
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_minimal
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_none_observed
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_qiime_tiny_test
FAILED skbio/diversity/alpha/tests/test_faith_pd.py::FaithPDTests::test_faith_pd_root_not_observed
FAILED skbio/diversity/alpha/tests/test_lladser.py::LladserTests::test_lladser_ci
FAILED skbio/diversity/alpha/tests/test_lladser.py::LladserTests::test_lladser_ci_f3
FAILED skbio/diversity/alpha/tests/test_lladser.py::LladserTests::test_lladser_pe
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_extra_tips
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_minimal_trees
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_otus_out_of_order
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_root_not_observed
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_identity
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_non_overlapping
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_symmetry
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_unweighted_unifrac_zero_counts
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_extra_tips
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_minimal_trees
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_normalized_root_not_observed
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_otus_out_of_order
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_root_not_observed
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_identity
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_identity_normalized
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_non_overlapping
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_non_overlapping_normalized
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_normalized
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_symmetry
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_symmetry_normalized
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_zero_counts
FAILED skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_weighted_unifrac_zero_counts_normalized
FAILED skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_empty
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_faith_pd
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_input_types
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_invalid_input
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_no_ids
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_observed_otus
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_optimized
FAILED skbio/diversity/tests/test_driver.py::AlphaDiversityTests::test_single_count_vector
FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_alt_pairwise_func
FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_invalid_input
FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_unweighted_unifrac
FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_weighted_unifrac
FAILED skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_weighted_unifrac_normalized
FAILED skbio/diversity/tests/test_driver.py::TestPartialBetaDiversity::test_id_pairs_as_iterable
FAILED skbio/diversity/tests/test_driver.py::TestPartialBetaDiversity::test_unweighted_unifrac_partial
FAILED skbio/diversity/tests/test_driver.py::TestPartialBetaDiversity::test_weighted_unifrac_partial_full
FAILED skbio/diversity/tests/test_util.py::ValidationTests::test_vectorize_counts_and_tree
FAILED skbio/io/format/tests/test_fasta.py::SnifferTests::test_positives - As...
FAILED skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_eq_from_different_source
FAILED skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_degap
FAILED skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_eq_from_different_source
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_eq_sequences_from_different_sources_compare_equal
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_boolean_vector_has_qual
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_int_has_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_iterable_of_mixed_has_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_numpy_index_has_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_slice_has_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_getitem_with_tuple_of_mixed_with_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_iter_has_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_reversed_has_positional_metadata
FAILED skbio/sequence/tests/test_sequence.py::TestSequence::test_slice_positional_metadata
FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_all_columns_explicit
FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_all_columns_implicit
FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_different_column_order
FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_single_column
FAILED skbio/stats/distance/tests/test_bioenv.py::BIOENVTests::test_bioenv_vegan_example
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_duplicate_dms
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_filepaths_as_input
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_id_lookup
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_many_filepaths_as_input
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_minimal_compatible_input
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_minimal_compatible_input_with_labels
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_na_p_value
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_reordered_distance_matrices
FAILED skbio/stats/distance/tests/test_mantel.py::PairwiseMantelTests::test_strict
FAILED skbio/stats/tests/test_subsample.py::SubsampleCountsTests::test_subsample_counts_nonrandom
FAILED skbio/stats/tests/test_subsample.py::SubsampleCountsTests::test_subsample_counts_without_replacement
FAILED skbio/stats/tests/test_subsample.py::ISubsampleTests::test_isubsample_simple
FAILED skbio/stats/tests/test_subsample.py::ISubsampleTests::test_per_sample_sequences_complex
FAILED skbio/stats/tests/test_subsample.py::ISubsampleTests::test_per_sample_sequences_min_seqs
===== 89 failed, 2233 passed, 30 skipped, 66 warnings in 167.61s (0:02:47) =====
E: pybuild pybuild:379: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build; python3.10 -m pytest
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 3.10" returned exit code 13
make: *** [debian/rules:14: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-12-30T07:59:03Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 39824
Build-Time: 270
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1758
Job: python-skbio_0.5.6-7
Machine Architecture: armhf
Package: python-skbio
Package-Time: 2060
Source-Version: 0.5.6-7
Space: 39824
Status: attempted
Version: 0.5.6-7
--------------------------------------------------------------------------------
Finished at 2022-12-30T07:59:03Z
Build needed 00:34:20, 39824k disk space