https://launchpad.net/ubuntu/+source/unifrac/0.10.0-3/+build/22312171 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-057 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 Buildd toolchain package versions: launchpad-buildd_204~508~ubuntu18.04.1 python3-lpbuildd_204~508~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 30 Nov 12:24:54 ntpdate[1758]: adjust time server 10.211.37.1 offset 0.000131 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22312171 --image-type chroot /home/buildd/filecache-default/b0c128df17a460089eca69348f06144377489985 Creating target for build PACKAGEBUILD-22312171 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22312171 Starting target for build PACKAGEBUILD-22312171 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22312171 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22312171 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22312171 Updating target for build PACKAGEBUILD-22312171 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 Packages [1400 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe amd64 Packages [13.3 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5561 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 Packages [199 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [67.9 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 Packages [1088 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [490 kB] Fetched 23.2 MB in 5s (4348 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libsepol1 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils ca-certificates cpp-11 dash debconf debianutils e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libtasn1-6 libtinfo6 libtsan0 libubsan1 libuuid1 libzstd1 linux-libc-dev lockfile-progs login logsave make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler sed sensible-utils tzdata usrmerge util-linux 93 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 75.7 MB of archives. After this operation, 355 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main amd64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpam0g amd64 1.4.0-10ubuntu1 [61.4 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcrypt-dev amd64 1:4.4.26-1 [112 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcrypt1 amd64 1:4.4.26-1 [82.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 base-files amd64 12ubuntu2 [63.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdutils amd64 1:2.37.2-4ubuntu1 [80.9 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 debianutils amd64 5.5-1 [77.5 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-3 [91.8 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 grep amd64 3.7-1 [156 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 login amd64 1:4.8.1-1ubuntu10 [188 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main amd64 libncurses6 amd64 6.3-1 [111 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main amd64 libncursesw6 amd64 6.3-1 [147 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 libtinfo6 amd64 6.3-1 [104 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-bin amd64 6.3-1 [184 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 sed amd64 4.8-1 [188 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 libblkid1 amd64 2.37.2-4ubuntu1 [103 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libpcre2-8-0 amd64 10.39-3 [220 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 libselinux1 amd64 3.3-1 [74.6 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 libmount1 amd64 2.37.2-4ubuntu1 [122 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 util-linux amd64 2.37.2-4ubuntu1 [1063 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-base all 6.3-1 [19.9 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 libgpg-error0 amd64 1.42-3 [68.1 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcrypt20 amd64 1.9.4-3ubuntu2 [515 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 libcc1-0 amd64 11.2.0-12ubuntu1 [53.8 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11-base amd64 11.2.0-12ubuntu1 [20.7 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-s1 amd64 11.2.0-12ubuntu1 [45.6 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 libgomp1 amd64 11.2.0-12ubuntu1 [117 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 libitm1 amd64 11.2.0-12ubuntu1 [30.0 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 libatomic1 amd64 11.2.0-12ubuntu1 [9998 B] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 libasan6 amd64 11.2.0-12ubuntu1 [2282 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 liblsan0 amd64 11.2.0-12ubuntu1 [976 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 libtsan0 amd64 11.2.0-12ubuntu1 [2259 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 libubsan1 amd64 11.2.0-12ubuntu1 [922 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 libquadmath0 amd64 11.2.0-12ubuntu1 [154 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 g++-11 amd64 11.2.0-12ubuntu1 [11.4 MB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++-11-dev amd64 11.2.0-12ubuntu1 [2098 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-11-dev amd64 11.2.0-12ubuntu1 [2532 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11 amd64 11.2.0-12ubuntu1 [20.1 MB] Get:39 http://ftpmaster.internal/ubuntu jammy/main amd64 cpp-11 amd64 11.2.0-12ubuntu1 [9962 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++6 amd64 11.2.0-12ubuntu1 [656 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libisl23 amd64 0.24-2 [728 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpc3 amd64 1.2.1-1 [46.9 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 libzstd1 amd64 1.4.8+dfsg-3 [324 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf0 amd64 2.37-10ubuntu1 [103 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf-nobfd0 amd64 2.37-10ubuntu1 [106 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 libbinutils amd64 2.37-10ubuntu1 [653 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-common amd64 2.37-10ubuntu1 [213 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils amd64 2.37-10ubuntu1 [3192 B] Get:49 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-x86-64-linux-gnu amd64 2.37-10ubuntu1 [2314 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 libapt-pkg6.0 amd64 2.3.13 [904 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgv amd64 2.2.27-2ubuntu1 [137 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 libidn2-0 amd64 2.3.2-2 [66.5 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main amd64 libp11-kit0 amd64 0.24.0-5 [252 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 libtasn1-6 amd64 4.18.0-4 [42.9 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libgnutls30 amd64 3.7.2-2ubuntu1 [957 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 libseccomp2 amd64 2.5.2-2ubuntu2 [48.3 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 apt amd64 2.3.13 [1387 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 libsepol2 amd64 3.3-1 [281 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main amd64 libsemanage-common all 3.3-1 [10.1 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main amd64 libsemanage2 amd64 3.3-1 [92.5 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main amd64 passwd amd64 1:4.8.1-1ubuntu10 [754 kB] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpam-modules-bin amd64 1.4.0-10ubuntu1 [37.4 kB] Get:63 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpam-modules amd64 1.4.0-10ubuntu1 [280 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main amd64 logsave amd64 1.46.4-1ubuntu1 [10.9 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main amd64 libext2fs2 amd64 1.46.4-1ubuntu1 [209 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main amd64 e2fsprogs amd64 1.46.4-1ubuntu1 [589 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 mount amd64 2.37.2-4ubuntu1 [114 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main amd64 libattr1 amd64 1:2.5.1-1 [13.3 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main amd64 libcom-err2 amd64 1.46.4-1ubuntu1 [10.1 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main amd64 libk5crypto3 amd64 1.18.3-7 [86.2 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main amd64 libkrb5support0 amd64 1.18.3-7 [32.2 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 libkrb5-3 amd64 1.18.3-7 [355 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 libgssapi-krb5-2 amd64 1.18.3-7 [143 kB] Get:74 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpam-runtime all 1.4.0-10ubuntu1 [40.2 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main amd64 libsmartcols1 amd64 2.37.2-4ubuntu1 [50.9 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main amd64 libuuid1 amd64 2.37.2-4ubuntu1 [23.8 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main amd64 libss2 amd64 1.46.4-1ubuntu1 [12.3 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main amd64 sensible-utils all 0.0.17 [20.1 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main amd64 usrmerge all 25ubuntu2 [54.7 kB] Get:80 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libssl3 amd64 3.0.0-1ubuntu1 [1896 kB] Get:81 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 openssl amd64 3.0.0-1ubuntu1 [1180 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main amd64 ca-certificates all 20211016 [148 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main amd64 libapparmor1 amd64 3.0.3-0ubuntu3 [37.8 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main amd64 libip4tc2 amd64 1.8.7-1ubuntu4 [19.8 kB] Get:85 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libkmod2 amd64 28-1ubuntu5 [48.0 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main amd64 libsqlite3-0 amd64 3.36.0-2 [641 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main amd64 tzdata all 2021e-1ubuntu1 [343 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm6 amd64 1.22-1 [35.2 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg amd64 2.2.27-2ubuntu1 [518 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgconf amd64 2.2.27-2ubuntu1 [93.9 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg-agent amd64 2.2.27-2ubuntu1 [209 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm-compat4 amd64 1.22-1 [6450 B] 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22312171 amd64 jammy-proposed -c chroot:build-PACKAGEBUILD-22312171 --arch=amd64 --dist=jammy-proposed --nolog -A unifrac_0.10.0-3.dsc Initiating build PACKAGEBUILD-22312171 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-057.buildd +==============================================================================+ | unifrac 0.10.0-3 (amd64) Tue, 30 Nov 2021 12:25:45 +0000 | +==============================================================================+ Package: unifrac Version: 0.10.0-3 Source Version: 0.10.0-3 Distribution: jammy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22312171/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- unifrac_0.10.0-3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/unifrac-aXJGp7/unifrac-0.10.0' with '<>' I: NOTICE: Log filtering will replace 'build/unifrac-aXJGp7' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-nDyYSt/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-nDyYSt/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nDyYSt/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-nDyYSt/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nDyYSt/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-nDyYSt/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (86.9 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libsepol1 Use 'apt autoremove' to remove it. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 654 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-nDyYSt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [654 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 654 B in 0s (58.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13434 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, python3-all-dev, python3-setuptools, python3-numpy, cython3, libhdf5-dev, hdf5-helpers, python3-h5py, python3-biom-format, python3-skbio, chrpath Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, python3-all-dev, python3-setuptools, python3-numpy, cython3, libhdf5-dev, hdf5-helpers, python3-h5py, python3-biom-format, python3-skbio, chrpath dpkg-deb: building package 'sbuild-build-depends-unifrac-dummy' in '/<>/resolver-nDyYSt/apt_archive/sbuild-build-depends-unifrac-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-unifrac-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-nDyYSt/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nDyYSt/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-nDyYSt/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nDyYSt/apt_archive ./ Sources [577 B] Get:5 copy:/<>/resolver-nDyYSt/apt_archive ./ Packages [646 B] Fetched 2186 B in 0s (59.4 kB/s) Reading package lists... Reading package lists... Install unifrac build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libsepol1 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file fonts-dejavu-core fonts-lyx gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67 libimagequant0 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblzf1 libmagic-mgc libmagic1 libmd0 libmpdec3 libnghttp2-14 libopenjp2-7 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libssw0 libsub-override-perl libsz2 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 libxslt1.1 m4 mailcap man-db media-types mime-support po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-backcall python3-biom-format python3-brotli python3-cachecontrol python3-certifi python3-chardet python3-click python3-colorama python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-h5py python3-h5py-serial python3-hdmedians python3-idna python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lib2to3 python3-lockfile python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-mpmath python3-msgpack python3-natsort python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pkg-resources python3-prompt-toolkit python3-ptyprocess python3-pygments python3-pyparsing python3-requests python3-scipy python3-setuptools python3-six python3-skbio python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-traitlets python3-tz python3-ufolib2 python3-urllib3 python3-wcwidth python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-dev python3.9-minimal unicode-data zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cython-doc dh-make flit python3-toml gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config libhdf5-doc libjs-jquery-ui-docs liblcms2-utils libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc python-biom-format-doc python-cycler-doc python-h5py-doc python-ipython-doc python-lockfile-doc python-lxml-doc dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gfortran python-numpy-doc python3-pytest python-pandas-doc python3-statsmodels python-pexpect-doc python-pil-doc python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python-skbio-doc python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc python3.10-venv python3.10-doc binfmt-support python3.9-venv python3.9-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-pytest python3-simplejson python3-psutil python3-bs4 python3-html5lib python3-pil.imagetk python3-tk python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-tables python3-jinja2 python3-numba python3-olefile python3-nose The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file fonts-dejavu-core fonts-lyx gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67 libimagequant0 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblzf1 libmagic-mgc libmagic1 libmd0 libmpdec3 libnghttp2-14 libopenjp2-7 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libssw0 libsub-override-perl libsz2 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 libxslt1.1 m4 mailcap man-db media-types mime-support po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-backcall python3-biom-format python3-brotli python3-cachecontrol python3-certifi python3-chardet python3-click python3-colorama python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-h5py python3-h5py-serial python3-hdmedians python3-idna python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lib2to3 python3-lockfile python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-mpmath python3-msgpack python3-natsort python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pkg-resources python3-prompt-toolkit python3-ptyprocess python3-pygments python3-pyparsing python3-requests python3-scipy python3-setuptools python3-six python3-skbio python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl python3-traitlets python3-tz python3-ufolib2 python3-urllib3 python3-wcwidth python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-dev python3.9-minimal sbuild-build-depends-unifrac-dummy unicode-data zlib1g-dev 0 upgraded, 190 newly installed, 0 to remove and 0 not upgraded. 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amd64 libldap-2.5-0 amd64 2.5.6+dfsg-1~exp1ubuntu1 [186 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 libnghttp2-14 amd64 1.43.0-1build1 [76.2 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build3 [58.3 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main amd64 libssh-4 amd64 0.9.6-1 [185 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main amd64 libcurl4 amd64 7.74.0-1.3ubuntu2 [273 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main amd64 libcurl4-openssl-dev amd64 7.74.0-1.3ubuntu2 [365 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main amd64 libdeflate0 amd64 1.8-1ubuntu1 [56.4 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main amd64 libexpat1-dev amd64 2.4.1-3 [147 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main amd64 libfreetype6 amd64 2.11.0+dfsg-1 [387 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main amd64 libgfortran5 amd64 11.2.0-12ubuntu1 [794 kB] Get:81 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jammy-proposed/main amd64 python3-dev amd64 3.9.7-4 [25.9 kB] Get:129 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3.10-dev amd64 3.10.0-5build1 [509 kB] Get:130 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-all-dev amd64 3.9.7-4 [924 B] Get:131 http://ftpmaster.internal/ubuntu jammy/main amd64 python3-appdirs all 1.4.4-1 [11.0 kB] Get:132 http://ftpmaster.internal/ubuntu jammy/main amd64 python3-attr all 20.3.0-1ubuntu1 [41.0 kB] Get:133 http://ftpmaster.internal/ubuntu jammy/universe amd64 python3-backcall all 0.2.0-2 [11.0 kB] Get:134 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-numpy amd64 1:1.21.4-2 [3968 kB] Get:135 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 python3-h5py-serial amd64 3.3.0-4ubuntu1 [1051 kB] Get:136 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 python3-h5py all 3.3.0-4ubuntu1 [4730 B] Get:137 http://ftpmaster.internal/ubuntu jammy/main amd64 python3-colorama all 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Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:amd64 (3.10.0-5build1) ... Setting up python3.10 (3.10.0-5build1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up libpython3.9-dev:amd64 (3.9.9-1build1) ... Setting up python3 (3.9.7-4) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-tz (2021.3-1) ... Setting up python3-natsort (7.1.0-1) ... Setting up python3-six (1.16.0-2) ... Setting up dh-autoreconf (20) ... Setting up python3-pil:amd64 (8.4.0-1) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-wcwidth (0.1.9+dfsg1-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... 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Setting up python3-ipython (7.27.0-1) ... Setting up libhdf5-dev (1.10.7+repack-4ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-h5py (3.3.0-4ubuntu1) ... Setting up python3-sklearn (0.23.2-5ubuntu4) ... Setting up python3-biom-format (2.1.10-2ubuntu1) ... Setting up python3-fonttools (4.27.1-1) ... Setting up python3-ufolib2 (0.11.1+dfsg1-1) ... Setting up python3-matplotlib (3.5.0-2) ... Setting up python3-skbio (0.5.6-5ubuntu1) ... Setting up sbuild-build-depends-unifrac-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic amd64 (x86_64) Toolchain package versions: binutils_2.37-10ubuntu1 dpkg-dev_1.20.9ubuntu2 g++-11_11.2.0-12ubuntu1 gcc-11_11.2.0-12ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-12ubuntu1 libstdc++6_11.2.0-12ubuntu1 linux-libc-dev_5.15.0-12.12 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-3ubuntu2 binutils_2.37-10ubuntu1 binutils-common_2.37-10ubuntu1 binutils-x86-64-linux-gnu_2.37-10ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-4ubuntu4 ca-certificates_20211016 chrpath_0.16-2 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python3-colorama_0.4.4-1 python3-cycler_0.11.0-1 python3-dateutil_2.8.1-6 python3-decorator_4.4.2-0ubuntu1 python3-dev_3.9.7-4 python3-distutils_3.9.9-2 python3-fonttools_4.27.1-1 python3-fs_2.4.12-1 python3-h5py_3.3.0-4ubuntu1 python3-h5py-serial_3.3.0-4ubuntu1 python3-hdmedians_0.14.2-1 python3-idna_2.10-1 python3-ipython_7.27.0-1 python3-jedi_0.18.0-1 python3-joblib_0.17.0-4ubuntu1 python3-kiwisolver_1.3.2-1 python3-lib2to3_3.9.9-2 python3-lockfile_1:0.12.2-2.2 python3-lxml_4.6.4-1 python3-lz4_3.1.3+dfsg-1build2 python3-matplotlib_3.5.0-2 python3-matplotlib-inline_0.1.3-1 python3-minimal_3.9.7-4 python3-mpmath_1.2.1-2 python3-msgpack_1.0.2-2 python3-natsort_7.1.0-1 python3-numpy_1:1.21.4-2 python3-packaging_21.3-1 python3-pandas_1.1.5+dfsg-2ubuntu1 python3-pandas-lib_1.1.5+dfsg-2ubuntu1 python3-parso_0.8.1-1 python3-pexpect_4.8.0-2ubuntu1 python3-pickleshare_0.7.5-5 python3-pil_8.4.0-1 python3-pkg-resources_59.2.0-1 python3-prompt-toolkit_3.0.22-1 python3-ptyprocess_0.7.0-2 python3-pygments_2.7.1+dfsg-2.1 python3-pyparsing_2.4.7-1 python3-requests_2.25.1+dfsg-2 python3-scipy_1.7.1-1ubuntu1 python3-setuptools_59.2.0-1 python3-six_1.16.0-2 python3-skbio_0.5.6-5ubuntu1 python3-sklearn_0.23.2-5ubuntu4 python3-sklearn-lib_0.23.2-5ubuntu4 python3-sympy_1.7.1-3 python3-threadpoolctl_2.1.0-1 python3-traitlets_5.1.1-1 python3-tz_2021.3-1 python3-ufolib2_0.11.1+dfsg1-1 python3-urllib3_1.26.5-1~exp1 python3-wcwidth_0.1.9+dfsg1-2 python3.10_3.10.0-5build1 python3.10-dev_3.10.0-5build1 python3.10-minimal_3.10.0-5build1 python3.9_3.9.9-1build1 python3.9-dev_3.9.9-1build1 python3.9-minimal_3.9.9-1build1 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-unifrac-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 systemd_248.3-1ubuntu8 systemd-sysv_248.3-1ubuntu8 systemd-timesyncd_248.3-1ubuntu8 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 unicode-data_14.0.0-1.1 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Sep 14 12:17:52 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./unifrac_0.10.0-3.dsc dpkg-source: info: extracting unifrac in /<> dpkg-source: info: unpacking unifrac_0.10.0.orig.tar.gz dpkg-source: info: unpacking unifrac_0.10.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-cython-post-clean.patch dpkg-source: info: applying Fix-Makefile.patch dpkg-source: info: applying remove-check-for-pkg-version.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22312171 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22312171 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22312171 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package unifrac dpkg-buildpackage: info: source version 0.10.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base:237: python3.10 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.10_unifrac/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:237: python3.9 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.9_unifrac/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it find . -name "*.o" -delete rm -rf .pybuild/ build/ sucpp/ssu unifrac/_api.cpp sucpp/test_su sucpp/test_api sucpp/libssu.so.0 sucpp/faithpd sucpp/libssu.so rm -rf unifrac.egg-info make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:237: python3.10 setup.py config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/unifrac/_api.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling unifrac/_api.pyx because it changed. [1/1] Cythonizing unifrac/_api.pyx running config I: pybuild base:237: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac copying unifrac/_methods.py -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac copying unifrac/_meta.py -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac copying unifrac/__init__.py -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac creating /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests copying unifrac/tests/test_methods.py -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests copying unifrac/tests/test_api.py -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests copying unifrac/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests creating /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e1.biom -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t2.newick -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e2.biom -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t1.newick -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.tre -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.biom -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/test.faith.exp -> /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data running build_ext Compiling SSU make[1]: Entering directory '/<>/sucpp' rm -f *.o ssu make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/<>/sucpp' building 'unifrac._api' extension creating build creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/sucpp creating build/temp.linux-x86_64-3.10/unifrac x86_64-linux-gnu-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=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.10 -c sucpp/api.cpp -o build/temp.linux-x86_64-3.10/sucpp/api.o -std=c++11 -I/usr/include/hdf5/serial sucpp/api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: sucpp/api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ sucpp/api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: sucpp/api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ sucpp/api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int x86_64-linux-gnu-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=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.10 -c unifrac/_api.cpp -o build/temp.linux-x86_64-3.10/unifrac/_api.o -std=c++11 -I/usr/include/hdf5/serial In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from unifrac/_api.cpp:675: /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 " \ | ^~~~~~~ unifrac/_api.cpp: In function ‘PyObject* __pyx_pf_7unifrac_4_api_ssu(PyObject*, PyObject*, PyObject*, PyObject*, bool, double, bool, unsigned int)’: unifrac/_api.cpp:3236:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3236 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_16; __pyx_t_9+=1) { | ~~~~~~~~~~^~~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/sucpp/api.o build/temp.linux-x86_64-3.10/unifrac/_api.o -Lsucpp/ -lssu -o /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/_api.cpython-310-x86_64-linux-gnu.so -std=c++11 I: pybuild base:237: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac copying unifrac/_methods.py -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac copying unifrac/_meta.py -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac copying unifrac/__init__.py -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac creating /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests copying unifrac/tests/test_methods.py -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests copying unifrac/tests/test_api.py -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests copying unifrac/tests/__init__.py -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests creating /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e1.biom -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t2.newick -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e2.biom -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t1.newick -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.tre -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.biom -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/test.faith.exp -> /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data running build_ext Compiling SSU make[1]: Entering directory '/<>/sucpp' rm -f *.o ssu make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/<>/sucpp' building 'unifrac._api' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/sucpp creating build/temp.linux-x86_64-3.9/unifrac x86_64-linux-gnu-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=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.9 -c sucpp/api.cpp -o build/temp.linux-x86_64-3.9/sucpp/api.o -std=c++11 -I/usr/include/hdf5/serial sucpp/api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: sucpp/api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ sucpp/api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: sucpp/api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ sucpp/api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int x86_64-linux-gnu-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=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.9 -c unifrac/_api.cpp -o build/temp.linux-x86_64-3.9/unifrac/_api.o -std=c++11 -I/usr/include/hdf5/serial In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from unifrac/_api.cpp:675: /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 " \ | ^~~~~~~ unifrac/_api.cpp: In function ‘PyObject* __pyx_pf_7unifrac_4_api_ssu(PyObject*, PyObject*, PyObject*, PyObject*, bool, double, bool, unsigned int)’: unifrac/_api.cpp:3236:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3236 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_16; __pyx_t_9+=1) { | ~~~~~~~~~~^~~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/sucpp/api.o build/temp.linux-x86_64-3.9/unifrac/_api.o -Lsucpp/ -lssu -o /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/_api.cpython-39-x86_64-linux-gnu.so -std=c++11 debian/rules override_dh_auto_test make[1]: Entering directory '/<>' LD_LIBRARY_PATH=:`pwd`/sucpp dh_auto_test -O --buildsystem=pybuild I: pybuild base:237: cd /<>/.pybuild/cpython3_3.10_unifrac/build; python3.10 -m unittest discover -v test_ssu_table_not_subset_tree (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_extra_tips (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_minimal_trees (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_otus_out_of_order (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_root_not_observed (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac_identity (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac_non_overlapping (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac_symmetry (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_extra_tips (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_normalized_root_not_observed (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_otus_out_of_order (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_root_not_observed (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_identity (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_identity_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_non_overlapping (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_non_overlapping_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_symmetry (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_symmetry_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_faith_pd (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_all_observed (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_biom_table_empty (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_extra_tips (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_invalid_input (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_minimal (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_none_observed (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_root_not_observed (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_series_name (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_table_not_subset_tree (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_zero_branches_omitted (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_meta_unifrac (unifrac.tests.test_api.UnifracAPITests) ... ok test_ssu_bad_method (unifrac.tests.test_api.UnifracAPITests) ... ok test_ssu_bad_table (unifrac.tests.test_api.UnifracAPITests) ... ok test_ssu_bad_tree (unifrac.tests.test_api.UnifracAPITests) ... ok test_unweighted_root_eval_issue_46 (unifrac.tests.test_api.UnifracAPITests) ... ok test_meta_unifrac (unifrac.tests.test_methods.StateUnifracTests) meta_unifrac should give correct result on sample trees ... ok test_meta_unifrac_alpha_not_generalized (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_bad_consolidation (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_bad_method (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_missing (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_no_method (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_unbalanced (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_unbalanced_weights (unifrac.tests.test_methods.StateUnifracTests) ... ok ---------------------------------------------------------------------- Ran 45 tests in 9.471s OK I: pybuild base:237: cd /<>/.pybuild/cpython3_3.9_unifrac/build; python3.9 -m unittest discover -v test_ssu_table_not_subset_tree (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_extra_tips (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_minimal_trees (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_otus_out_of_order (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_root_not_observed (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac_identity (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac_non_overlapping (unifrac.tests.test_api.EdgeCasesTests) ... ok test_unweighted_unifrac_symmetry (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_extra_tips (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_normalized_root_not_observed (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_otus_out_of_order (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_root_not_observed (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_identity (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_identity_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_non_overlapping (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_non_overlapping_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_symmetry (unifrac.tests.test_api.EdgeCasesTests) ... ok test_weighted_unifrac_symmetry_normalized (unifrac.tests.test_api.EdgeCasesTests) ... ok test_faith_pd (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_all_observed (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_biom_table_empty (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_extra_tips (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_invalid_input (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_minimal (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_none_observed (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_root_not_observed (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_series_name (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_table_not_subset_tree (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_faith_pd_zero_branches_omitted (unifrac.tests.test_api.FaithPDEdgeCasesTests) ... ok test_meta_unifrac (unifrac.tests.test_api.UnifracAPITests) ... ok test_ssu_bad_method (unifrac.tests.test_api.UnifracAPITests) ... ok test_ssu_bad_table (unifrac.tests.test_api.UnifracAPITests) ... ok test_ssu_bad_tree (unifrac.tests.test_api.UnifracAPITests) ... ok test_unweighted_root_eval_issue_46 (unifrac.tests.test_api.UnifracAPITests) ... ok test_meta_unifrac (unifrac.tests.test_methods.StateUnifracTests) meta_unifrac should give correct result on sample trees ... ok test_meta_unifrac_alpha_not_generalized (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_bad_consolidation (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_bad_method (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_missing (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_no_method (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_unbalanced (unifrac.tests.test_methods.StateUnifracTests) ... ok test_meta_unifrac_unbalanced_weights (unifrac.tests.test_methods.StateUnifracTests) ... ok ---------------------------------------------------------------------- Ran 45 tests in 10.825s OK make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py install --root /<>/debian/python3-unifrac running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext Compiling SSU make[1]: Entering directory '/<>/sucpp' rm -f *.o ssu make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/<>/sucpp' running install_lib creating /<>/debian/python3-unifrac creating /<>/debian/python3-unifrac/usr creating /<>/debian/python3-unifrac/usr/lib creating /<>/debian/python3-unifrac/usr/lib/python3.10 creating /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages creating /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/_methods.py -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/_api.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/_meta.py -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/__init__.py -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac creating /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/__pycache__ copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/__pycache__/_meta.cpython-310.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/__pycache__ copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/__pycache__/_methods.cpython-310.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/__pycache__ copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/__pycache__/__init__.cpython-310.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/__pycache__ creating /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/test_methods.py -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests creating /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/e1.biom -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/t2.newick -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/e2.biom -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/t1.newick -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/crawford.tre -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/crawford.biom -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/test.faith.exp -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/test_api.py -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/__init__.py -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests creating /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/__pycache__/__init__.cpython-310.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/__pycache__/test_methods.cpython-310.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/__pycache__/test_api.cpython-310.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/__pycache__ byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/_methods.py to _methods.cpython-310.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/_meta.py to _meta.cpython-310.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/test_methods.py to test_methods.cpython-310.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/test_api.py to test_api.cpython-310.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/__init__.py to __init__.cpython-310.pyc running install_egg_info running egg_info creating unifrac.egg-info writing unifrac.egg-info/PKG-INFO writing dependency_links to unifrac.egg-info/dependency_links.txt writing requirements to unifrac.egg-info/requires.txt writing top-level names to unifrac.egg-info/top_level.txt writing manifest file 'unifrac.egg-info/SOURCES.txt' reading manifest file 'unifrac.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'unifrac.egg-info/SOURCES.txt' Copying unifrac.egg-info to /<>/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac-0.10.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:237: /usr/bin/python3 setup.py install --root /<>/debian/python3-unifrac running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext Compiling SSU make[1]: Entering directory '/<>/sucpp' rm -f *.o ssu make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/<>/sucpp' make[1]: Entering directory '/<>/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/<>/sucpp' running install_lib creating /<>/debian/python3-unifrac/usr/lib/python3.9 creating /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages creating /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/_methods.py -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/_meta.py -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/_api.cpython-39-x86_64-linux-gnu.so -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/__init__.py -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac creating /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/__pycache__ copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/__pycache__/_methods.cpython-39.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/__pycache__ copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/__pycache__/_meta.cpython-39.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/__pycache__ copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/__pycache__/__init__.cpython-39.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/__pycache__ creating /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/test_methods.py -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests creating /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/e1.biom -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/t2.newick -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/e2.biom -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/t1.newick -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/crawford.tre -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/crawford.biom -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/test.faith.exp -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/test_api.py -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/__init__.py -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests creating /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/__pycache__ copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/__pycache__/test_api.cpython-39.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/__pycache__ copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/__pycache__/test_methods.cpython-39.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/__pycache__ copying /<>/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/__pycache__/__init__.cpython-39.pyc -> /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/__pycache__ byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/_methods.py to _methods.cpython-39.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/_meta.py to _meta.cpython-39.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/__init__.py to __init__.cpython-39.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/test_methods.py to test_methods.cpython-39.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/test_api.py to test_api.cpython-39.pyc byte-compiling /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/__init__.py to __init__.cpython-39.pyc running install_egg_info running egg_info writing unifrac.egg-info/PKG-INFO writing dependency_links to unifrac.egg-info/dependency_links.txt writing requirements to unifrac.egg-info/requires.txt writing top-level names to unifrac.egg-info/top_level.txt reading manifest file 'unifrac.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'unifrac.egg-info/SOURCES.txt' Copying unifrac.egg-info to /<>/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac-0.10.0.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/<>' chrpath -d debian/libssu-tools/usr/bin/ssu chrpath -d debian/libssu-tools/usr/bin/faithpd chrpath -d debian/libssu0/usr/lib/x86_64-linux-gnu/libssu.so.0 make[1]: Leaving directory '/<>' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild debugedit: debian/libssu-tools/usr/bin/ssu: Unknown DWARF DW_FORM_0x1f21 debugedit: debian/python3-unifrac/usr/lib/python3/dist-packages/unifrac/_api.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 38f2fc1ea06132ed50f573dd7d5f0d9630eddeee 4c69a35ef486bf25605228896349c22ea089b4b7 d56ded2fa3cc03dee160a06964d8732fa4debe1b debugedit: debian/python3-unifrac/usr/lib/python3/dist-packages/unifrac/_api.cpython-39-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 79ea597d7a0065aa731f428c2bc4ebda3684f621 debugedit: debian/libssu-tools/usr/bin/faithpd: Unknown DWARF DW_FORM_0x1f21 ad27a25e5e2b42fa4ddf43e191bd5f78a465f95d dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: Depends field of package libssu-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing python3-unifrac (in debian/python3-unifrac); do_strip: , oemstrip: pkgstriptranslations: processing libssu-dev (in debian/libssu-dev); do_strip: , oemstrip: pkgstriptranslations: processing libssu-tools-dbgsym (in debian/.debhelper/libssu-tools/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libssu0 (in debian/libssu0); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-unifrac/DEBIAN/control, package python3-unifrac, directory debian/python3-unifrac Searching for duplicated docs in dependency libssu0... symlinking changelog.Debian.gz in python3-unifrac to file in libssu0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-unifrac ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-unifrac' in '../python3-unifrac_0.10.0-3_amd64.deb'. pkgstripfiles: processing control file: debian/libssu-dev/DEBIAN/control, package libssu-dev, directory debian/libssu-dev INFO: pkgstripfiles: waiting for lock (libssu-dev) ... pkgstripfiles: processing control file: debian/libssu0/DEBIAN/control, package libssu0, directory debian/libssu0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libssu0 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libssu0' in '../libssu0_0.10.0-3_amd64.deb'. INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libssu0-dbgsym (in debian/.debhelper/libssu0/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-unifrac-dbgsym (in debian/.debhelper/python3-unifrac/dbgsym-root); do_strip: , oemstrip: Searching for duplicated docs in dependency libssu0... symlinking changelog.Debian.gz in libssu-dev to file in libssu0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libssu-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libssu-dev' in '../libssu-dev_0.10.0-3_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libssu0/dbgsym-root/DEBIAN/control, package libssu0-dbgsym, directory debian/.debhelper/libssu0/dbgsym-root dpkg-deb: building package 'libssu0-dbgsym' in 'debian/.debhelper/scratch-space/build-libssu0/libssu0-dbgsym_0.10.0-3_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/python3-unifrac/dbgsym-root/DEBIAN/control, package python3-unifrac-dbgsym, directory debian/.debhelper/python3-unifrac/dbgsym-root dpkg-deb: building package 'python3-unifrac-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-unifrac/python3-unifrac-dbgsym_0.10.0-3_amd64.deb'. INFO: pkgstriptranslations version 149 Renaming libssu0-dbgsym_0.10.0-3_amd64.deb to libssu0-dbgsym_0.10.0-3_amd64.ddeb Renaming python3-unifrac-dbgsym_0.10.0-3_amd64.deb to python3-unifrac-dbgsym_0.10.0-3_amd64.ddeb pkgstriptranslations: processing libssu-tools (in debian/libssu-tools); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libssu-tools/DEBIAN/control, package libssu-tools, directory debian/libssu-tools Searching for duplicated docs in dependency libssu0... symlinking changelog.Debian.gz in libssu-tools to file in libssu0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libssu-tools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libssu-tools' in '../libssu-tools_0.10.0-3_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libssu-tools/dbgsym-root/DEBIAN/control, package libssu-tools-dbgsym, directory debian/.debhelper/libssu-tools/dbgsym-root dpkg-deb: building package 'libssu-tools-dbgsym' in 'debian/.debhelper/scratch-space/build-libssu-tools/libssu-tools-dbgsym_0.10.0-3_amd64.deb'. Renaming libssu-tools-dbgsym_0.10.0-3_amd64.deb to libssu-tools-dbgsym_0.10.0-3_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../unifrac_0.10.0-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-11-30T12:31:29Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ unifrac_0.10.0-3_amd64.changes: ------------------------------- Format: 1.8 Date: Tue, 14 Sep 2021 17:39:15 +0530 Source: unifrac Binary: libssu-dev libssu-tools libssu0 python3-unifrac Built-For-Profiles: noudeb Architecture: amd64 Version: 0.10.0-3 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steffen Moeller Description: libssu-dev - high-performance phylogenetic diversity calculations (dev) libssu-tools - high-performance phylogenetic diversity calculations (binaries) libssu0 - high-performance phylogenetic diversity calculations (lib) python3-unifrac - high-performance phylogenetic diversity calculations Changes: unifrac (0.10.0-3) unstable; urgency=medium . * Team Upload. * d/rules: better clean-up * removed -mfma to avoid illegal instruction error on older machines Checksums-Sha1: 4b3e33f79ca87696593136b076c10ec3b944dead 10294 libssu-dev_0.10.0-3_amd64.deb 97371b33c2300a30af299519d071b6a8df95d660 1324554 libssu-tools-dbgsym_0.10.0-3_amd64.ddeb bd15e1a86f93715367f52aa13865dfea06c334fb 1620734 libssu-tools_0.10.0-3_amd64.deb 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12851 science optional unifrac_0.10.0-3_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: unifrac Binary: libssu-dev libssu-tools libssu-tools-dbgsym libssu0 libssu0-dbgsym python3-unifrac python3-unifrac-dbgsym Architecture: amd64 Version: 0.10.0-3 Checksums-Md5: 501e6fd80210a7cf6eea6b9522a9daab 10294 libssu-dev_0.10.0-3_amd64.deb 92f33cc8e4c521ef92e7315791475867 1324554 libssu-tools-dbgsym_0.10.0-3_amd64.ddeb e21842eab64c34cc71c2c5f10fed7394 1620734 libssu-tools_0.10.0-3_amd64.deb 43a9411d793d67221076834bcc9b8468 666652 libssu0-dbgsym_0.10.0-3_amd64.ddeb dac96087f3dba6f18f7357bc69ee6b4f 53892 libssu0_0.10.0-3_amd64.deb 14213baec3c6bc7ee35b12323b966c5c 812382 python3-unifrac-dbgsym_0.10.0-3_amd64.ddeb e491478b55cdba3573c8905545fbda55 133272 python3-unifrac_0.10.0-3_amd64.deb Checksums-Sha1: 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libssu0-dbgsym_0.10.0-3_amd64.ddeb b40cf80f35644e732a9b2e2f7954a750fc8bb9edb8b445d38def491c38a809d4 53892 libssu0_0.10.0-3_amd64.deb e0b0c1d7c5ac68a410c3491f3ddc77c9616eba84f72fc5125e331bfff8a5492a 812382 python3-unifrac-dbgsym_0.10.0-3_amd64.ddeb 46cc874b33ec418eb73ed75f02dcfebd196995f62bfc180b7ef4ffb79f35f31e 133272 python3-unifrac_0.10.0-3_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Tue, 30 Nov 2021 12:31:28 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu2), base-passwd (= 3.5.52), bash (= 5.1-3ubuntu2), binutils (= 2.37-10ubuntu1), binutils-common (= 2.37-10ubuntu1), binutils-x86-64-linux-gnu (= 2.37-10ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-4ubuntu4), ca-certificates (= 20211016), chrpath (= 0.16-2), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-12ubuntu1), cython3 (= 0.29.24-0ubuntu3), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.5.2ubuntu1), debianutils (= 5.5-1), debugedit (= 1:5.0-3), dh-autoreconf (= 20), dh-exec (= 0.23.4build1), dh-python (= 5.20211114), dh-strip-nondeterminism (= 1.12.1-1), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.20.9ubuntu2), dpkg-dev (= 1.20.9ubuntu2), dwz (= 0.14-1build1), file (= 1:5.41-2), findutils (= 4.8.0-1ubuntu2), fonts-dejavu-core (= 2.37-2build1), fonts-lyx (= 2.3.6-1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-12ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-12ubuntu1), gcc-11-base (= 11.2.0-12ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hdf5-helpers (= 1.10.7+repack-4ubuntu1), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libaec-dev (= 1.0.6-1), libaec0 (= 1.0.6-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-12ubuntu1), libatomic1 (= 11.2.0-12ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-10ubuntu1), libblas3 (= 3.9.0-3ubuntu3), libblkid1 (= 2.37.2-4ubuntu1), libbrotli1 (= 1.0.9-2build4), libbsd0 (= 0.11.3-1ubuntu3), libbz2-1.0 (= 1.0.8-4ubuntu4), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-12ubuntu1), libcom-err2 (= 1.46.4-1ubuntu1), libcrypt-dev (= 1:4.4.26-1), libcrypt1 (= 1:4.4.26-1), libctf-nobfd0 (= 2.37-10ubuntu1), libctf0 (= 2.37-10ubuntu1), libcurl4 (= 7.74.0-1.3ubuntu2), libcurl4-openssl-dev (= 7.74.0-1.3ubuntu2), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.5.2ubuntu1), libdeflate0 (= 1.8-1ubuntu1), libdpkg-perl (= 1.20.9ubuntu2), libdw1 (= 0.186-1), libedit2 (= 3.1-20210910-1), libelf1 (= 0.186-1), libexpat1 (= 2.4.1-3), libexpat1-dev (= 2.4.1-3), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.1-1), libfreetype6 (= 2.11.0+dfsg-1), libfribidi0 (= 1.0.8-2ubuntu2), libgcc-11-dev (= 11.2.0-12ubuntu1), libgcc-s1 (= 11.2.0-12ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgfortran5 (= 11.2.0-12ubuntu1), libglib2.0-0 (= 2.70.1-1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgnutls30 (= 3.7.2-2ubuntu1), libgomp1 (= 11.2.0-12ubuntu1), libgpg-error0 (= 1.42-3), libgraphite2-3 (= 1.3.14-1build1), libgssapi-krb5-2 (= 1.18.3-7), libharfbuzz0b (= 2.7.4-1ubuntu2), libhdf5-103-1 (= 1.10.7+repack-4ubuntu1), libhdf5-cpp-103-1 (= 1.10.7+repack-4ubuntu1), libhdf5-dev (= 1.10.7+repack-4ubuntu1), libhdf5-fortran-102 (= 1.10.7+repack-4ubuntu1), libhdf5-hl-100 (= 1.10.7+repack-4ubuntu1), libhdf5-hl-cpp-100 (= 1.10.7+repack-4ubuntu1), libhdf5-hl-fortran-100 (= 1.10.7+repack-4ubuntu1), libhogweed6 (= 3.7.3-1build1), libicu67 (= 67.1-7ubuntu1), libidn2-0 (= 2.3.2-2), libimagequant0 (= 2.12.2-1.1build1), libisl23 (= 0.24-2), libitm1 (= 11.2.0-12ubuntu1), libjbig0 (= 2.1-3.1build2), libjpeg-dev (= 8c-2ubuntu8), libjpeg-turbo8 (= 2.1.1-0ubuntu1), libjpeg-turbo8-dev (= 2.1.1-0ubuntu1), libjpeg8 (= 8c-2ubuntu8), libjpeg8-dev (= 8c-2ubuntu8), libjs-jquery (= 3.5.1+dfsg+~3.5.5-8), libjs-jquery-ui (= 1.13.0+dfsg-1), libjs-sphinxdoc (= 4.3.1-1), libjs-underscore (= 1.9.1~dfsg-4), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), liblapack3 (= 3.9.0-3ubuntu3), liblbfgsb0 (= 3.0+dfsg.3-9), liblcms2-2 (= 2.12~rc1-2build1), libldap-2.5-0 (= 2.5.6+dfsg-1~exp1ubuntu1), liblsan0 (= 11.2.0-12ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzf1 (= 3.6-3), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmd0 (= 1.0.4-1), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2build1), libmpfr6 (= 4.1.0-3build2), libncurses6 (= 6.3-1), libncursesw6 (= 6.3-1), libnettle8 (= 3.7.3-1build1), libnghttp2-14 (= 1.43.0-1build1), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libopenjp2-7 (= 2.4.0-3), libp11-kit0 (= 0.24.0-5), libpam-modules (= 1.4.0-10ubuntu1), libpam-modules-bin (= 1.4.0-10ubuntu1), libpam-runtime (= 1.4.0-10ubuntu1), libpam0g (= 1.4.0-10ubuntu1), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.4-1), libpng16-16 (= 1.6.37-3build4), libprocps8 (= 2:3.3.17-5ubuntu3), libpsl5 (= 0.21.0-1.2build1), libpython3-all-dev (= 3.9.7-4), libpython3-dev (= 3.9.7-4), libpython3-stdlib (= 3.9.7-4), libpython3.10 (= 3.10.0-5build1), libpython3.10-dev (= 3.10.0-5build1), libpython3.10-minimal (= 3.10.0-5build1), libpython3.10-stdlib (= 3.10.0-5build1), libpython3.9 (= 3.9.9-1build1), libpython3.9-dev (= 3.9.9-1build1), libpython3.9-minimal (= 3.9.9-1build1), libpython3.9-stdlib (= 3.9.9-1build1), libqhull-r8.0 (= 2020.2-4), libquadmath0 (= 11.2.0-12ubuntu1), libraqm0 (= 0.7.0-4), libreadline8 (= 8.1-2build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libsasl2-2 (= 2.1.27+dfsg2-2build1), libsasl2-modules-db (= 2.1.27+dfsg2-2build1), libseccomp2 (= 2.5.2-2ubuntu2), libselinux1 (= 3.3-1), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu1), libsqlite3-0 (= 3.36.0-2), libssh-4 (= 0.9.6-1), libssl-dev (= 3.0.0-1ubuntu1), libssl1.1 (= 1.1.1l-1ubuntu1), libssl3 (= 3.0.0-1ubuntu1), libssw0 (= 1.1-13), libstdc++-11-dev (= 11.2.0-12ubuntu1), libstdc++6 (= 11.2.0-12ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 248.3-1ubuntu8), libsz2 (= 1.0.6-1), libtasn1-6 (= 4.18.0-4), libtiff5 (= 4.3.0-2), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libtsan0 (= 11.2.0-12ubuntu1), libubsan1 (= 11.2.0-12ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 248.3-1ubuntu8), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libwebp6 (= 0.6.1-2.1build1), libwebpdemux2 (= 0.6.1-2.1build1), libwebpmux3 (= 0.6.1-2.1build1), libxau6 (= 1:1.0.9-1build4), libxcb1 (= 1.14-3ubuntu2), libxdmcp6 (= 1:1.1.3-0ubuntu4), libxml2 (= 2.9.12+dfsg-5), libxslt1.1 (= 1.1.34-4build1), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.0-12.12), login (= 1:4.8.1-1ubuntu10), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 16), m4 (= 1.4.18-5ubuntu1), mailcap (= 3.70ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), media-types (= 4.0.0), mime-support (= 3.66), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), openssl (= 3.0.0-1ubuntu1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-5ubuntu3), python-matplotlib-data (= 3.5.0-2), python3 (= 3.9.7-4), python3-all (= 3.9.7-4), python3-all-dev (= 3.9.7-4), python3-appdirs (= 1.4.4-1), python3-attr (= 20.3.0-1ubuntu1), python3-backcall (= 0.2.0-2), python3-biom-format (= 2.1.10-2ubuntu1), python3-brotli (= 1.0.9-2build4), python3-cachecontrol (= 0.12.10-1), python3-certifi (= 2020.6.20-1), python3-chardet (= 4.0.0-1), python3-click (= 8.0.2-1), python3-colorama (= 0.4.4-1), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.1-6), python3-decorator (= 4.4.2-0ubuntu1), python3-dev (= 3.9.7-4), python3-distutils (= 3.9.9-2), python3-fonttools (= 4.27.1-1), python3-fs (= 2.4.12-1), python3-h5py (= 3.3.0-4ubuntu1), python3-h5py-serial (= 3.3.0-4ubuntu1), python3-hdmedians (= 0.14.2-1), python3-idna (= 2.10-1), python3-ipython (= 7.27.0-1), python3-jedi (= 0.18.0-1), python3-joblib (= 0.17.0-4ubuntu1), python3-kiwisolver (= 1.3.2-1), python3-lib2to3 (= 3.9.9-2), python3-lockfile (= 1:0.12.2-2.2), python3-lxml (= 4.6.4-1), python3-lz4 (= 3.1.3+dfsg-1build2), python3-matplotlib (= 3.5.0-2), python3-matplotlib-inline (= 0.1.3-1), python3-minimal (= 3.9.7-4), python3-mpmath (= 1.2.1-2), python3-msgpack (= 1.0.2-2), python3-natsort (= 7.1.0-1), python3-numpy (= 1:1.21.4-2), python3-packaging (= 21.3-1), python3-pandas (= 1.1.5+dfsg-2ubuntu1), python3-pandas-lib (= 1.1.5+dfsg-2ubuntu1), python3-parso (= 0.8.1-1), python3-pexpect (= 4.8.0-2ubuntu1), python3-pickleshare (= 0.7.5-5), python3-pil (= 8.4.0-1), python3-pkg-resources (= 59.2.0-1), python3-prompt-toolkit (= 3.0.22-1), python3-ptyprocess (= 0.7.0-2), python3-pygments (= 2.7.1+dfsg-2.1), python3-pyparsing (= 2.4.7-1), python3-requests (= 2.25.1+dfsg-2), python3-scipy (= 1.7.1-1ubuntu1), python3-setuptools (= 59.2.0-1), python3-six (= 1.16.0-2), python3-skbio (= 0.5.6-5ubuntu1), python3-sklearn (= 0.23.2-5ubuntu4), python3-sklearn-lib (= 0.23.2-5ubuntu4), python3-sympy (= 1.7.1-3), python3-threadpoolctl (= 2.1.0-1), python3-traitlets (= 5.1.1-1), python3-tz (= 2021.3-1), python3-ufolib2 (= 0.11.1+dfsg1-1), python3-urllib3 (= 1.26.5-1~exp1), python3-wcwidth (= 0.1.9+dfsg1-2), python3.10 (= 3.10.0-5build1), python3.10-dev (= 3.10.0-5build1), python3.10-minimal (= 3.10.0-5build1), python3.9 (= 3.9.9-1build1), python3.9-dev (= 3.9.9-1build1), python3.9-minimal (= 3.9.9-1build1), readline-common (= 8.1-2build1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), tzdata (= 2021e-1ubuntu1), unicode-data (= 14.0.0-1.1), util-linux (= 2.37.2-4ubuntu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1631621355" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libssu-dev_0.10.0-3_amd64.deb ----------------------------- new Debian package, version 2.0. size 10294 bytes: control archive=1010 bytes. 1086 bytes, 23 lines control 581 bytes, 9 lines md5sums Package: libssu-dev Source: unifrac Version: 0.10.0-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 53 Depends: libssu0 (= 0.10.0-3) Section: libdevel Priority: optional Homepage: https://github.com/biocore/unifrac Description: high-performance phylogenetic diversity calculations (dev) The de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac. This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. . This package contains the static library and header files. drwxr-xr-x root/root 0 2021-09-14 12:09 ./ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/include/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/include/sucpp/ -rw-r--r-- root/root 3318 2019-07-08 20:22 ./usr/include/sucpp/affinity.hpp -rw-r--r-- root/root 10499 2019-07-08 20:22 ./usr/include/sucpp/api.hpp -rw-r--r-- root/root 3410 2019-07-08 20:22 ./usr/include/sucpp/biom.hpp -rw-r--r-- root/root 1056 2019-07-08 20:22 ./usr/include/sucpp/cmd.hpp -rw-r--r-- root/root 1098 2019-07-08 20:22 ./usr/include/sucpp/task_parameters.hpp -rw-r--r-- root/root 4660 2019-07-08 20:22 ./usr/include/sucpp/tree.hpp -rw-r--r-- root/root 3523 2019-07-08 20:22 ./usr/include/sucpp/unifrac.hpp -rw-r--r-- root/root 6101 2019-07-08 20:22 ./usr/include/sucpp/unifrac_task.hpp drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2021-09-14 12:09 ./usr/lib/x86_64-linux-gnu/libssu.so -> libssu.so.0 drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/libssu-dev/ lrwxrwxrwx root/root 0 2021-09-14 12:09 ./usr/share/doc/libssu-dev/changelog.Debian.gz -> ../libssu0/changelog.Debian.gz -rw-r--r-- root/root 2743 2021-09-14 12:07 ./usr/share/doc/libssu-dev/copyright libssu-tools_0.10.0-3_amd64.deb ------------------------------- new Debian package, version 2.0. size 1620734 bytes: control archive=939 bytes. 1173 bytes, 23 lines control 295 bytes, 5 lines md5sums Package: libssu-tools Source: unifrac Version: 0.10.0-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7182 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), libsz2 (>= 1.0.6), zlib1g (>= 1:1.1.4), libssu0 Section: science Priority: optional Homepage: https://github.com/biocore/unifrac Description: high-performance phylogenetic diversity calculations (binaries) The de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac. This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. . This package contains target binaries ssu and faithpd drwxr-xr-x root/root 0 2021-09-14 12:09 ./ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/bin/ -rwxr-xr-x root/root 3658512 2021-09-14 12:09 ./usr/bin/faithpd -rwxr-xr-x root/root 3678992 2021-09-14 12:09 ./usr/bin/ssu drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/libssu-tools/ lrwxrwxrwx root/root 0 2021-09-14 12:09 ./usr/share/doc/libssu-tools/changelog.Debian.gz -> ../libssu0/changelog.Debian.gz -rw-r--r-- root/root 2743 2021-09-14 12:07 ./usr/share/doc/libssu-tools/copyright drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/man/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/man/man1/ -rw-r--r-- root/root 456 2021-09-14 12:09 ./usr/share/man/man1/faithpd.1.gz -rw-r--r-- root/root 1330 2021-09-14 12:09 ./usr/share/man/man1/ssu.1.gz libssu0_0.10.0-3_amd64.deb -------------------------- new Debian package, version 2.0. size 53892 bytes: control archive=990 bytes. 1144 bytes, 23 lines control 213 bytes, 3 lines md5sums 29 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: libssu0 Source: unifrac Version: 0.10.0-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 137 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libhdf5-103-1, libhdf5-cpp-103-1 (>= 1.10.5), libstdc++6 (>= 11) Section: libs Priority: optional Homepage: https://github.com/biocore/unifrac Description: high-performance phylogenetic diversity calculations (lib) The de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac. This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. . This package contains the shared library. drwxr-xr-x root/root 0 2021-09-14 12:09 ./ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 125088 2021-09-14 12:09 ./usr/lib/x86_64-linux-gnu/libssu.so.0 drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/libssu0/ -rw-r--r-- root/root 329 2021-09-14 12:09 ./usr/share/doc/libssu0/changelog.Debian.gz -rw-r--r-- root/root 2743 2021-09-14 12:07 ./usr/share/doc/libssu0/copyright python3-unifrac_0.10.0-3_amd64.deb ---------------------------------- new Debian package, version 2.0. size 133272 bytes: control archive=1817 bytes. 1257 bytes, 23 lines control 1960 bytes, 21 lines md5sums 267 bytes, 12 lines * postinst #!/bin/sh 416 bytes, 12 lines * prerm #!/bin/sh Package: python3-unifrac Source: unifrac Version: 0.10.0-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 730 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libssu0 (>= 0.10.0), libstdc++6 (>= 11), cython3, python3 (<< 3.11), python3 (>= 3.9~), python3-biom-format, python3-h5py-serial, python3-numpy, python3-skbio, python3:any Section: python Priority: optional Homepage: https://github.com/biocore/unifrac Description: high-performance phylogenetic diversity calculations The de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac. This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. . This package contains the Python3 module. drwxr-xr-x root/root 0 2021-09-14 12:09 ./ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/python3/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac-0.10.0.egg-info/ -rw-r--r-- root/root 10423 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac-0.10.0.egg-info/PKG-INFO -rw-r--r-- root/root 1 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac-0.10.0.egg-info/dependency_links.txt -rw-r--r-- root/root 100 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac-0.10.0.egg-info/requires.txt -rw-r--r-- root/root 8 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac-0.10.0.egg-info/top_level.txt drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac/ -rw-r--r-- root/root 733 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac/__init__.py -rw-r--r-- root/root 214608 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac/_api.cpython-310-x86_64-linux-gnu.so -rw-r--r-- root/root 214608 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac/_api.cpython-39-x86_64-linux-gnu.so -rw-r--r-- root/root 3824 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/_meta.py -rw-r--r-- root/root 15416 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/_methods.py drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac/tests/ -rw-r--r-- root/root 349 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/__init__.py drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/lib/python3/dist-packages/unifrac/tests/data/ -rw-r--r-- root/root 137185 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/crawford.biom -rw-r--r-- root/root 9394 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/crawford.tre -rw-r--r-- root/root 33840 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/e1.biom -rw-r--r-- root/root 33840 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/e2.biom -rw-r--r-- root/root 35 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/t1.newick -rw-r--r-- root/root 27 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/t2.newick -rw-r--r-- root/root 276 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/data/test.faith.exp -rw-r--r-- root/root 33069 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/test_api.py -rw-r--r-- root/root 3687 2019-07-08 20:22 ./usr/lib/python3/dist-packages/unifrac/tests/test_methods.py drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/doc/python3-unifrac/ lrwxrwxrwx root/root 0 2021-09-14 12:09 ./usr/share/doc/python3-unifrac/changelog.Debian.gz -> ../libssu0/changelog.Debian.gz -rw-r--r-- root/root 2743 2021-09-14 12:07 ./usr/share/doc/python3-unifrac/copyright drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-09-14 12:09 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 118 2021-09-14 12:07 ./usr/share/lintian/overrides/python3-unifrac +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 218 Distribution: jammy-proposed Host Architecture: amd64 Install-Time: 123 Job: unifrac_0.10.0-3.dsc Machine Architecture: amd64 Package: unifrac Package-Time: 344 Source-Version: 0.10.0-3 Space: n/a Status: successful Version: 0.10.0-3 -------------------------------------------------------------------------------- Finished at 2021-11-30T12:31:29Z Build needed 00:05:44, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22312171 Scanning for processes to kill in build PACKAGEBUILD-22312171