Wed May 22 18:13:32 UTC 2024 I: starting to build umap-learn/unstable/amd64 on jenkins on '2024-05-22 18:13' Wed May 22 18:13:32 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/8449/console.log Wed May 22 18:13:32 UTC 2024 I: Downloading source for unstable/umap-learn=0.5.4+dfsg-1 --2024-05-22 18:13:32-- http://deb.debian.org/debian/pool/main/u/umap-learn/umap-learn_0.5.4%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2357 (2.3K) [text/prs.lines.tag] Saving to: ‘umap-learn_0.5.4+dfsg-1.dsc’ 0K .. 100% 224M=0s 2024-05-22 18:13:32 (224 MB/s) - ‘umap-learn_0.5.4+dfsg-1.dsc’ saved [2357/2357] Wed May 22 18:13:32 UTC 2024 I: umap-learn_0.5.4+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: umap-learn Binary: umap-learn Architecture: all Version: 0.5.4+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/lmcinnes/umap Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/umap-learn Vcs-Git: https://salsa.debian.org/med-team/umap-learn.git Testsuite: autopkgtest Testsuite-Triggers: file, mayavi2, python3-all, python3-matplotlib, python3-numba, python3-numpy, python3-seaborn, python3-sklearn, xauth, xvfb Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, python3-numpy, python3-scipy, python3-sklearn, python3-numba, python3-pynndescent , python3-tqdm , python3-pytest Package-List: umap-learn deb science optional arch=all Checksums-Sha1: a0b36144e2273f9fb13c8bfbb26f0950bc8d2d0c 1463296 umap-learn_0.5.4+dfsg.orig.tar.xz 73dde040fd89999404af6e0e79cf830cfaefec79 6472 umap-learn_0.5.4+dfsg-1.debian.tar.xz Checksums-Sha256: 2609156df2d9dd634938a577db9818fa0a9eed3e388713487f5e08d38a825a63 1463296 umap-learn_0.5.4+dfsg.orig.tar.xz 69950dd08071a9a768c7e3e178ca092b7af745879bc735138965e55d053f743f 6472 umap-learn_0.5.4+dfsg-1.debian.tar.xz Files: 74b68896e87f4bc3b006b5f4df6743be 1463296 umap-learn_0.5.4+dfsg.orig.tar.xz 2760f631a0ed9b888e7ec79a713f2f91 6472 umap-learn_0.5.4+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVMdF8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH1DhAAmAozTvXdN1RdZjpySO6ZntSmZvm2HgwZ IuOesD353+OCX4soRTUNAfAvr8B/36W7gyg8L6jFSejA2imlUje6XN5Zl+GU2YAE OIAMdosHQ4buKRac8vrK55Bq1CDN6OrLu5MgZWA8H6S7bbquhlNSgHvNPyAJQtjr Z3CpdMtUDBTczIKEKjJlMNH2p13tZHwiM8Tg2ACWyuPTBoxwPNj3itl/x+L0DBy7 2jNmb0CFjHg9H3Z1TV2gaTqAST5eIAPQNSoovg5F0mUZWeA5ibFgPKPj+0Tv1X3F djBhF2EzIVZm/GJ/7xKZDQAZWfiTmw+izpYb4o3iNR9SvPRLqESc7Z85ZhHevKlT yE6Wdwv9/mH1VnrjI0epeMW5FDiKG67OLF0pgamOPy4LClapqNOwMqPX0IvRgjwR oHKA+fhOS0W1ie4UzrLRgcH8beFc0X44oTQ6EczbXYsA5DZU91t40t3wGVFZs8R9 WGElMajImdHBddZ2Q319NZo3umjgBYdblE+DRJ9dKuHRThunuveutSlkcNWBB42k pQPkd8Fk7xROqbPnlyaMsu+BpORPK07UIh+jEdFRxo6iXk4gIw/+UVQ2lUvVJk9K rTBzT/8/LINYS9Mohy9HCt0IUPJEzDNi6tSwVD1c8QQXwvb70hHI8VFBWmueR79Z YqKj9U2fT8c= =JuOk -----END PGP SIGNATURE----- Wed May 22 18:13:32 UTC 2024 I: Checking whether the package is not for us Wed May 22 18:13:32 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Wed May 22 18:13:32 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Wed May 22 18:22:52 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 24 12:36:33 -12 2025 I: pbuilder-time-stamp: 1750811793 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [umap-learn_0.5.4+dfsg-1.dsc] I: copying [./umap-learn_0.5.4+dfsg.orig.tar.xz] I: copying [./umap-learn_0.5.4+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 9 05:55:43 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./umap-learn_0.5.4+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting umap-learn in umap-learn-0.5.4+dfsg dpkg-source: info: unpacking umap-learn_0.5.4+dfsg.orig.tar.xz dpkg-source: info: unpacking umap-learn_0.5.4+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-and-fix-incompatible-tests.patch dpkg-source: info: applying skip_tests_needing_tensorflow.patch dpkg-source: info: applying 3ca4cf8620e25ceb8b4602648f4092d7a904a282.patch dpkg-source: info: applying fix_further_tests.patch dpkg-source: info: applying fix-example.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/944957/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='66ca61d875624c4b8e8d137c2cb76d56' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='944957' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TXYrpe8H/pbuilderrc_5uul --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TXYrpe8H/b1 --logfile b1/build.log umap-learn_0.5.4+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 23 14:06 /bin -> usr/bin I: user script /srv/workspace/pbuilder/944957/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, python3-numpy, python3-scipy, python3-sklearn, python3-numba, python3-pynndescent, python3-tqdm, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19718 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-numba; however: Package python3-numba is not installed. pbuilder-satisfydepends-dummy depends on python3-pynndescent; however: Package python3-pynndescent is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcom-err2{a} libcurl4t64{a} libdata-optlist-perl{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhwloc15{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} libllvm14t64{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libparams-util-perl{a} libpfm4{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtool{a} libuchardet0{a} libxml2{a} libz3-4{a} llvm-14{a} llvm-14-linker-tools{a} llvm-14-runtime{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-decorator{a} python3-distutils{a} python3-iniconfig{a} python3-joblib{a} python3-lib2to3{a} python3-llvmlite{a} python3-minimal{a} python3-numba{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pynndescent{a} python3-pytest{a} python3-scipy{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-threadpoolctl{a} python3-tqdm{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support ca-certificates curl krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules llvm-14-dev lynx numba-doc psmisc publicsuffix python3-matplotlib python3-pil python3-pip python3-psutil python3-pygments python3-simplejson systemd wget 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 113 MB of archives. After unpacking 529 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsub-prototype-perl amd64 0.03-2+b2 [9744 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 63 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libllvm14t64 amd64 1:14.0.6-20 [21.9 MB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git32-g0d4ed0e-1 [341 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2021.11.0-2 [48.6 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2021.11.0-2 [14.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2021.11.0-2 [87.6 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 llvm-14-runtime amd64 1:14.0.6-20 [481 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 llvm-14-linker-tools amd64 1:14.0.6-20 [1292 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 llvm-14 amd64 1:14.0.6-20 [11.8 MB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-llvmlite amd64 0.42.0-1+b1 [180 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.11.4-10 [19.5 MB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-numba amd64 0.59.0+dfsg-2 [1766 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-1 [6606 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-1 [2247 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 python3-pynndescent amd64 0.5.8-2 [42.6 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.1.2-1 [246 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.66.4-1 [90.8 kB] Fetched 113 MB in 24s (4744 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19718 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21026 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/umap-learn-0.5.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../umap-learn_0.5.4+dfsg-1_source.changes dpkg-buildpackage: info: source package umap-learn dpkg-buildpackage: info: source version 0.5.4+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/parametric_umap.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/validation.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/aligned_umap.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/__init__.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/spectral.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/umap_.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/layouts.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/utils.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/sparse.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/plot.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap copying umap/distances.py -> /build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build/umap debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/umap-learn-0.5.4+dfsg' dh_auto_test -- --system=custom --test-args="PYTHONPATH={build_dir} {interpreter} -m pytest" I: pybuild base:311: PYTHONPATH=/build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build python3.11 -m pytest ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-8.1.2, pluggy-1.5.0 rootdir: /build/reproducible-path/umap-learn-0.5.4+dfsg collected 209 items umap/tests/test_aligned_umap.py ....s [ 2%] umap/tests/test_chunked_parallel_spatial_metric.py sssssssssssssssssssss [ 12%] sssssssssssssssssssss [ 22%] umap/tests/test_composite_models.py .s.. [ 24%] umap/tests/test_data_input.py . [ 24%] umap/tests/test_densmap.py .s.. [ 26%] umap/tests/test_parametric_umap.py sssssss [ 30%] umap/tests/test_plot.py s [ 30%] umap/tests/test_spectral.py .. [ 31%] umap/tests/test_umap_get_feature_names_out.py .... [ 33%] umap/tests/test_umap_metrics.py ............s.................s......... [ 52%] .. [ 53%] umap/tests/test_umap_nn.py ..sssssss.. [ 58%] umap/tests/test_umap_on_iris.py ............ [ 64%] umap/tests/test_umap_ops.py ...FFFFFFFF.....F.. [ 73%] umap/tests/test_umap_repeated_data.py ......... [ 77%] umap/tests/test_umap_trustworthiness.py .......... [ 82%] umap/tests/test_umap_validation_params.py .............................. [ 97%] ...... [100%] =================================== FAILURES =================================== ____________________ test_disconnected_data[True-jaccard-1] ____________________ num_isolates = 1, metric = 'jaccard', force_approximation = True @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError ____________________ test_disconnected_data[True-jaccard-5] ____________________ num_isolates = 5, metric = 'jaccard', force_approximation = True @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError ___________________ test_disconnected_data[True-hellinger-1] ___________________ num_isolates = 1, metric = 'hellinger', force_approximation = True @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError ___________________ test_disconnected_data[True-hellinger-5] ___________________ num_isolates = 5, metric = 'hellinger', force_approximation = True @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError ___________________ test_disconnected_data[False-jaccard-1] ____________________ num_isolates = 1, metric = 'jaccard', force_approximation = False @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError ___________________ test_disconnected_data[False-jaccard-5] ____________________ num_isolates = 5, metric = 'jaccard', force_approximation = False @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError __________________ test_disconnected_data[False-hellinger-1] ___________________ num_isolates = 1, metric = 'hellinger', force_approximation = False @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError __________________ test_disconnected_data[False-hellinger-5] ___________________ num_isolates = 5, metric = 'hellinger', force_approximation = False @pytest.mark.parametrize("num_isolates", [1, 5]) @pytest.mark.parametrize("metric", ["jaccard", "hellinger"]) @pytest.mark.parametrize("force_approximation", [True, False]) def test_disconnected_data(num_isolates, metric, force_approximation): options = [False, True] disconnected_data = np.random.choice(a=options, size=(10, 30), p=[0.6, 1 - 0.6]) # Add some disconnected data for the corner case test disconnected_data = np.vstack( [disconnected_data, np.zeros((num_isolates, 30), dtype="bool")] ) new_columns = np.zeros((num_isolates + 10, num_isolates), dtype="bool") for i in range(num_isolates): new_columns[10 + i, i] = True disconnected_data = np.hstack([disconnected_data, new_columns]) > with pytest.warns(None) as w: umap/tests/test_umap_ops.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = WarningsChecker(record=True), expected_warning = None, match_expr = None def __init__( self, expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning, match_expr: Optional[Union[str, Pattern[str]]] = None, *, _ispytest: bool = False, ) -> None: check_ispytest(_ispytest) super().__init__(_ispytest=True) msg = "exceptions must be derived from Warning, not %s" if isinstance(expected_warning, tuple): for exc in expected_warning: if not issubclass(exc, Warning): raise TypeError(msg % type(exc)) expected_warning_tup = expected_warning elif isinstance(expected_warning, type) and issubclass( expected_warning, Warning ): expected_warning_tup = (expected_warning,) else: > raise TypeError(msg % type(expected_warning)) E TypeError: exceptions must be derived from Warning, not /usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError ____________________________ test_umap_update_large ____________________________ iris = {'data': array([[5.1, 3.5, 1.4, 0.2], [4.9, 3. , 1.4, 0.2], [4.7, 3.2, 1.3, 0.2], [4.6, 3.1, 1.5,... width (cm)', 'petal length (cm)', 'petal width (cm)'], 'filename': 'iris.csv', 'data_module': 'sklearn.datasets.data'} iris_subset_model_large = UMAP(force_approximation_algorithm=True, min_dist=0.01, n_neighbors=10, random_state=42, tqdm_kwds={'bar_format': '{desc}: {percentage:3.0f}%| {bar} {n_fmt}/{total_fmt} [{elapsed}]', 'desc': 'Epochs completed', 'disable': True}) iris_selection = array([False, True, True, False, True, True, True, True, True, True, True, True, True, False, True,... True, True, True, True, True, False, True, False, True, True, False, False, False, True, False]) iris_model_large = UMAP(force_approximation_algorithm=True, min_dist=0.01, n_neighbors=10, random_state=42, tqdm_kwds={'bar_format': '{desc}: {percentage:3.0f}%| {bar} {n_fmt}/{total_fmt} [{elapsed}]', 'desc': 'Epochs completed', 'disable': True}) def test_umap_update_large( iris, iris_subset_model_large, iris_selection, iris_model_large ): new_data = iris.data[~iris_selection] new_model = iris_subset_model_large new_model.update(new_data) comparison_graph = scipy.sparse.vstack( [ iris_model_large.graph_[iris_selection], iris_model_large.graph_[~iris_selection], ] ) comparison_graph = scipy.sparse.hstack( [comparison_graph[:, iris_selection], comparison_graph[:, ~iris_selection]] ) error = np.sum(np.abs((new_model.graph_ - comparison_graph).data)) > assert error < 3.0 # Higher error tolerance based on approx nearest neighbors E assert 17.72839 < 3.0 umap/tests/test_umap_ops.py:262: AssertionError =============================== warnings summary =============================== umap/__init__.py:36 /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/__init__.py:36: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources umap/tests/test_chunked_parallel_spatial_metric.py:234 /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/tests/test_chunked_parallel_spatial_metric.py:234: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.benchmark( umap/tests/test_chunked_parallel_spatial_metric.py:258 /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/tests/test_chunked_parallel_spatial_metric.py:258: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.benchmark( umap/tests/test_chunked_parallel_spatial_metric.py:288 /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/tests/test_chunked_parallel_spatial_metric.py:288: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.benchmark( umap/tests/test_chunked_parallel_spatial_metric.py:312 /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/tests/test_chunked_parallel_spatial_metric.py:312: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.benchmark( umap/plot.py:20 /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/plot.py:20: UserWarning: The umap.plot package requires extra plotting libraries to be installed. You can install these via pip using pip install umap-learn[plot] or via conda using conda install pandas matplotlib datashader bokeh holoviews colorcet scikit-image warn( umap/tests/test_aligned_umap.py::test_aligned_update /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/aligned_umap.py:195: NumbaTypeSafetyWarning: unsafe cast from int64 to int32. Precision may be lost. if i in relation_dict: umap/tests/test_composite_models.py: 7 warnings umap/tests/test_densmap.py: 3 warnings umap/tests/test_umap_on_iris.py: 8 warnings umap/tests/test_umap_ops.py: 2 warnings umap/tests/test_umap_trustworthiness.py: 9 warnings /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism. warn(f"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.") umap/tests/test_umap_get_feature_names_out.py::test_get_feature_names_out_featureunion umap/tests/test_umap_get_feature_names_out.py::test_get_feature_names_out_featureunion umap/tests/test_umap_repeated_data.py::test_repeated_points_large_n umap/tests/test_umap_validation_params.py::test_umap_too_many_neighbors_warns umap/tests/test_umap_validation_params.py::test_umap_inverse_transform_fails_expectedly /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:2433: UserWarning: n_neighbors is larger than the dataset size; truncating to X.shape[0] - 1 warn( umap/tests/test_umap_metrics.py::test_hellinger /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/tests/test_umap_metrics.py:413: RuntimeWarning: invalid value encountered in sqrt dist_matrix = np.sqrt(dist_matrix) umap/tests/test_umap_on_iris.py::test_precomputed_transform_on_iris umap/tests/test_umap_on_iris.py::test_precomputed_sparse_transform_on_iris umap/tests/test_umap_ops.py::test_multi_component_layout_precomputed umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[True-1] umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[False-1] umap/tests/test_umap_trustworthiness.py::test_sparse_precomputed_metric_umap_trustworthiness umap/tests/test_umap_validation_params.py::test_umap_update_bad_params /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:1857: UserWarning: using precomputed metric; inverse_transform will be unavailable warn("using precomputed metric; inverse_transform will be unavailable") umap/tests/test_umap_on_iris.py::test_precomputed_transform_on_iris umap/tests/test_umap_on_iris.py::test_precomputed_sparse_transform_on_iris /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:2959: UserWarning: Transforming new data with precomputed metric. We are assuming the input data is a matrix of distances from the new points to the points in the training set. If the input matrix is sparse, it should contain distances from the new points to their nearest neighbours or approximate nearest neighbours in the training set. warn( umap/tests/test_umap_ops.py::test_multi_component_layout umap/tests/test_umap_ops.py::test_multi_component_layout_precomputed /usr/lib/python3/dist-packages/sklearn/manifold/_spectral_embedding.py:301: UserWarning: Graph is not fully connected, spectral embedding may not work as expected. warnings.warn( umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[True-1] /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:126: UserWarning: A few of your vertices were disconnected from the manifold. This shouldn't cause problems. Disconnection_distance = 1 has removed 3 edges. It has only fully disconnected 1 vertices. Use umap.utils.disconnected_vertices() to identify them. warn( umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[False-1] /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:126: UserWarning: A few of your vertices were disconnected from the manifold. This shouldn't cause problems. Disconnection_distance = 1 has removed 32 edges. It has only fully disconnected 1 vertices. Use umap.utils.disconnected_vertices() to identify them. warn( umap/tests/test_umap_validation_params.py::test_umap_inverse_transform_fails_expectedly /build/reproducible-path/umap-learn-0.5.4+dfsg/umap/umap_.py:1879: UserWarning: gradient function is not yet implemented for dice distance metric; inverse_transform will be unavailable warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED umap/tests/test_umap_ops.py::test_disconnected_data[True-jaccard-1] - ... FAILED umap/tests/test_umap_ops.py::test_disconnected_data[True-jaccard-5] - ... FAILED umap/tests/test_umap_ops.py::test_disconnected_data[True-hellinger-1] FAILED umap/tests/test_umap_ops.py::test_disconnected_data[True-hellinger-5] FAILED umap/tests/test_umap_ops.py::test_disconnected_data[False-jaccard-1] FAILED umap/tests/test_umap_ops.py::test_disconnected_data[False-jaccard-5] FAILED umap/tests/test_umap_ops.py::test_disconnected_data[False-hellinger-1] FAILED umap/tests/test_umap_ops.py::test_disconnected_data[False-hellinger-5] FAILED umap/tests/test_umap_ops.py::test_umap_update_large - assert 17.72839 ... ====== 9 failed, 138 passed, 62 skipped, 56 warnings in 321.63s (0:05:21) ====== E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: PYTHONPATH=/build/reproducible-path/umap-learn-0.5.4+dfsg/.pybuild/cpython3_3.11/build python3.11 -m pytest dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest" returned exit code 13 make[1]: *** [debian/rules:16: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/umap-learn-0.5.4+dfsg' make: *** [debian/rules:12: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/944957 and its subdirectories Wed May 22 18:22:53 UTC 2024 W: No second build log, what happened?