https://launchpad.net/ubuntu/+archive/test-rebuild-20240502-noble/+build/28273980 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-s390x-004 5.4.0-181-generic #201-Ubuntu SMP Thu Mar 28 15:39:22 UTC 2024 s390x Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 14 May 07:15:26 ntpdate[1952]: adjust time server 10.211.37.1 offset -0.000320 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28273980 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-28273980 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28273980 Starting target for build PACKAGEBUILD-28273980 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28273980 'deb http://ftpmaster.internal/ubuntu noble main universe' Overriding sources.list in build-PACKAGEBUILD-28273980 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28273980 Updating target for build PACKAGEBUILD-28273980 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1324 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main Translation-en [513 kB] Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.2 MB] Get:5 http://ftpmaster.internal/ubuntu noble/universe Translation-en [5982 kB] Fetched 22.3 MB in 8s (2871 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc-13-s390x-linux-gnu gcc-14-base gcc-s390x-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-s390x-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 172 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 108 MB of archives. After this operation, 76.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1.1build1 [197 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3build3 [73.1 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1build1 [85.9 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu2 [149 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5-3 s390x 1.20.1-6ubuntu2 [360 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libk5crypto3 s390x 1.20.1-6ubuntu2 [90.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5support0 s390x 1.20.1-6ubuntu2 [34.7 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libacl1 s390x 2.3.2-1build1 [18.0 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libapparmor1 s390x 4.0.0-beta3-0ubuntu3 [50.8 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.4-2build2 [15.8 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libaudit1 s390x 1:3.1.2-2.1build1 [48.9 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libblkid1 s390x 2.39.3-9ubuntu6 [128 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libcap2 s390x 1:2.66-5ubuntu2 [31.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4build1 [119 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt1 s390x 1:4.4.36-4build1 [88.9 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build2 [75.6 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libgcrypt20 s390x 1.10.3-2build1 [501 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x liblzma5 s390x 5.6.1+really5.4.5-1 [135 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2build1 [341 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libkmod2 s390x 31+20240202-2ubuntu7 [56.4 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x liblz4-1 s390x 1.9.4-1build1 [79.4 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu2 [245 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libselinux1 s390x 3.5-2ubuntu2 [84.8 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libmount1 s390x 2.39.3-9ubuntu6 [138 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-7 [764 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm6t64 s390x 1.23-5.1build1 [36.5 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm-compat4t64 s390x 1.23-5.1build1 [6890 B] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.38t64 s390x 5.38.2-3.2build2 [5006 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x perl s390x 5.38.2-3.2build2 [231 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x perl-base s390x 5.38.2-3.2build2 [1968 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu5 [15.8 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libtext-iconv-perl s390x 1.7-8build3 [13.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libtext-charwidth-perl s390x 0.04-11build3 [9518 B] Get:39 http://ftpmaster.internal/ubuntu noble/universe s390x libnss-nisplus s390x 1.3-5build1 [23.8 kB] Get:40 http://ftpmaster.internal/ubuntu noble/universe s390x libnss-nis s390x 3.1-0ubuntu7 [28.3 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu8 [20.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu7 [66.4 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu8 [1629 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu8 [2847 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu8 [654 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x openssl s390x 3.0.13-0ubuntu3 [1009 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd-shared s390x 255.4-1ubuntu8 [2131 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu4 [264 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libssl3t64 s390x 3.0.13-0ubuntu3 [1675 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x systemd-sysv s390x 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x systemd s390x 255.4-1ubuntu8 [3533 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd0 s390x 255.4-1ubuntu8 [443 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu5 [57.2 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.3-5ubuntu5 [289 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main s390x libnettle8t64 s390x 3.9.1-2.2build1 [210 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main s390x libhogweed6t64 s390x 3.9.1-2.2build1 [204 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-4ubuntu2 [320 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2build1 [550 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu3 [944 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libapt-pkg6.0t64 s390x 2.7.14build2 [1014 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x bzip2 s390x 1.0.8-5.1 [35.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libbz2-1.0 s390x 1.0.8-5.1 [40.0 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x gcc-14-base s390x 14-20240412-0ubuntu1 [47.6 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 14-20240412-0ubuntu1 [36.0 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 14-20240412-0ubuntu1 [905 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libudev1 s390x 255.4-1ubuntu8 [178 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2build1 [24.1 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu2 [75.9 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main s390x libgmp10 s390x 2:6.3.0+dfsg-2ubuntu6 [337 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.6-1build1 [23.1 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.7-2build1 [67.3 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x libtasn1-6 s390x 4.19.0-3build1 [48.5 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libdebconfclient0 s390x 0.271ubuntu3 [11.4 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3build1 [51.5 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libassuan0 s390x 2.5.6-1build1 [38.3 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu2 [747 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x gpg s390x 2.4.4-2ubuntu17 [589 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libreadline8t64 s390x 8.2-4build1 [171 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x readline-common all 8.2-4build1 [56.5 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu2 [161 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu2 [117 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main s390x gpg-agent s390x 2.4.4-2ubuntu17 [240 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x gpgconf s390x 2.4.4-2ubuntu17 [111 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x pinentry-curses s390x 1.2.1-3ubuntu5 [37.6 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x libnpth0t64 s390x 1.6-3.1build1 [8204 B] Get:88 http://ftpmaster.internal/ubuntu noble/main s390x gpgv s390x 2.4.4-2ubuntu17 [165 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x libseccomp2 s390x 2.5.5-1ubuntu3 [53.4 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x apt-utils s390x 2.7.14build2 [214 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x apt s390x 2.7.14build2 [1390 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main s390x debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.3-5ubuntu5 [69.8 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4build1 [54.1 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu3 [142 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main s390x libjson-c5 s390x 0.17-1build1 [37.2 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main s390x libuuid1 s390x 2.39.3-9ubuntu6 [35.9 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main s390x libfdisk1 s390x 2.39.3-9ubuntu6 [151 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main s390x mount s390x 2.39.3-9ubuntu6 [119 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu4 [22.9 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-31.31 [1593 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main s390x base-files s390x 13ubuntu10 [73.7 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17build1 [90.2 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x bash s390x 5.2.21-2ubuntu4 [845 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x bsdutils s390x 1:2.39.3-9ubuntu6 [96.5 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x coreutils s390x 9.4-3ubuntu6 [1483 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.35+dfsg-3build1 [269 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x dpkg s390x 1.22.6ubuntu6 [1278 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x dash s390x 0.5.12-6ubuntu5 [95.0 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1build1 [188 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main s390x findutils s390x 4.9.0-5build1 [305 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-4build1 [173 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main s390x gzip s390x 1.12-1ubuntu3 [107 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main s390x hostname s390x 3.23+nmu2ubuntu2 [11.2 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu2 [198 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x sed s390x 4.9-2build1 [198 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x util-linux s390x 2.39.3-9ubuntu6 [1142 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-6ubuntu3 [34.8 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu4 [22.6 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu4 [234 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu4 [614 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x optipng s390x 0.7.8+ds-1build2 [114 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main s390x libpng16-16t64 s390x 1.6.43-5build1 [200 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x init s390x 1.66ubuntu1 [6188 B] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x libsmartcols1 s390x 2.39.3-9ubuntu6 [68.2 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main s390x uuid-runtime s390x 2.39.3-9ubuntu6 [33.4 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main s390x libattr1 s390x 1:2.5.2-1build1 [11.7 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main s390x libmd0 s390x 1.1.0-2build1 [24.6 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2build1 [315 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build5 [96.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu3 [857 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu3 [59.8 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu4 [17.2 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20240123-1build1 [133 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x procps s390x 2:4.0.4-4ubuntu3 [724 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main s390x krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main s390x tzdata all 2024a-2ubuntu1 [273 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main s390x bsdextrautils s390x 2.39.3-9ubuntu6 [76.3 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main s390x libgpm2 s390x 1.20.7-11 [14.7 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main s390x libip4tc2 s390x 1.8.10-3ubuntu2 [24.2 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x libjansson4 s390x 2.14-2build2 [33.2 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x psmisc s390x 23.7-1build1 [178 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main s390x xz-utils s390x 5.6.1+really5.4.5-1 [269 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main s390x advancecomp s390x 2.5-1build1 [205 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-4ubuntu2 [98.4 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-4ubuntu2 [100 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu2 [2270 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-4ubuntu2 [479 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-4ubuntu2 [3042 B] Get:160 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-4ubuntu2 [217 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-4ubuntu2 [14.2 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240412-0ubuntu1 [1188 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240412-0ubuntu1 [151 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240412-0ubuntu1 [31.1 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240412-0ubuntu1 [9398 B] Get:166 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240412-0ubuntu1 [3003 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-23ubuntu4 [14.5 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-23ubuntu4 [472 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-23ubuntu4 [2494 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-23ubuntu4 [1004 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240412-0ubuntu1 [49.9 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-23ubuntu4 [1030 B] Get:173 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-23ubuntu4 [48.9 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main s390x libisl23 s390x 0.26-3build1 [713 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main s390x libmpfr6 s390x 4.2.1-1build1 [322 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main s390x libmpc3 s390x 1.3.1-1build1 [58.4 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-23ubuntu4 [19.1 MB] Get:178 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-23ubuntu4 [11.3 MB] Get:179 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-23ubuntu4 [9939 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:181 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:182 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:183 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:184 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:185 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:186 http://ftpmaster.internal/ubuntu noble/main s390x dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:187 http://ftpmaster.internal/ubuntu noble/main s390x libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main s390x patch s390x 2.7.6-7build3 [113 kB] Get:189 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build2 [196 kB] Get:190 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] Get:191 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.33-1 [31.9 kB] Get:192 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.33-1 [67.5 kB] Get:193 http://ftpmaster.internal/ubuntu noble/main s390x liblockfile-bin s390x 1.17-1build3 [11.6 kB] Get:194 http://ftpmaster.internal/ubuntu noble/main s390x liblockfile1 s390x 1.17-1build3 [7028 B] Get:195 http://ftpmaster.internal/ubuntu noble/main s390x lockfile-progs s390x 0.1.19build2 [8406 B] Preconfiguring packages ... Fetched 108 MB in 49s (2186 kB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../libtirpc-dev_1.3.4+ds-1.1build1_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../libnsl-dev_1.3.0-3build3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../libnsl2_1.3.0-3build3_s390x.deb ... Unpacking libnsl2:s390x (1.3.0-3build3) over (1.3.0-2build2) ... dpkg: libtirpc3:s390x: dependency problems, but removing anyway as you requested: libnss-nisplus:s390x depends on libtirpc3 (>= 1.0.2). (Reading database ... 13395 files and directories currently installed.) Removing libtirpc3:s390x (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:s390x. 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Unpacking perl-modules-5.38 (5.38.2-3.2build2) ... dpkg: libdb5.3:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libdb5.3. libpam-modules:s390x depends on libdb5.3. apt-utils depends on libdb5.3. (Reading database ... 14813 files and directories currently installed.) Removing libdb5.3:s390x (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:s390x. (Reading database ... 14807 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_s390x.deb ... Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-7) ... dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm6 (>= 1.21). libgdbm-compat4:s390x depends on libgdbm6 (>= 1.16). (Reading database ... 14813 files and directories currently installed.) Removing libgdbm6:s390x (1.23-3) ... Selecting previously unselected package libgdbm6t64:s390x. 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Unpacking libc-dev-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../6-rpcsvc-proto_1.4.2-0ubuntu7_s390x.deb ... Unpacking rpcsvc-proto (1.4.2-0ubuntu7) over (1.4.2-0ubuntu6) ... Preparing to unpack .../7-libc6-dev_2.39-0ubuntu8_s390x.deb ... Unpacking libc6-dev:s390x (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../8-libc6_2.39-0ubuntu8_s390x.deb ... Unpacking libc6:s390x (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc6:s390x (2.39-0ubuntu8) ... (Reading database ... 15345 files and directories currently installed.) Preparing to unpack .../libc-bin_2.39-0ubuntu8_s390x.deb ... Unpacking libc-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc-bin (2.39-0ubuntu8) ... (Reading database ... 15345 files and directories currently installed.) Preparing to unpack .../openssl_3.0.13-0ubuntu3_s390x.deb ... Unpacking openssl (3.0.13-0ubuntu3) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_255.4-1ubuntu8_s390x.deb ... Unpacking libsystemd-shared:s390x (255.4-1ubuntu8) over (253.5-1ubuntu6) ... Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu4_s390x.deb ... Unpacking libcryptsetup12:s390x (2:2.7.0-1ubuntu4) over (2:2.6.1-4ubuntu3) ... dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15344 files and directories currently installed.) Removing libssl3:s390x (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:s390x. (Reading database ... 15333 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_s390x.deb ... Unpacking libssl3t64:s390x (3.0.13-0ubuntu3) ... Setting up libssl3t64:s390x (3.0.13-0ubuntu3) ... (Reading database ... 15346 files and directories currently installed.) Preparing to unpack .../systemd-dev_255.4-1ubuntu8_all.deb ... Unpacking systemd-dev (255.4-1ubuntu8) over (253.5-1ubuntu6) ... 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Unpacking systemd (255.4-1ubuntu8) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu8_s390x.deb ... 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Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:s390x (1:4.4.36-4build1) ... Setting up libasan8:s390x (14-20240412-0ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1build1) ... Setting up libkrb5-3:s390x (1.20.1-6ubuntu2) ... Setting up liblockfile1:s390x (1.17-1build3) ... Setting up libperl5.38t64:s390x (5.38.2-3.2build2) ... Setting up libbinutils:s390x (2.42-4ubuntu2) ... Setting up libisl23:s390x (0.26-3build1) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build2) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:s390x (14-20240412-0ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libitm1:s390x (14-20240412-0ubuntu1) ... Setting up libctf0:s390x (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14build2) ... Setting up binutils-s390x-linux-gnu (2.42-4ubuntu2) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up binutils (2.42-4ubuntu2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-23ubuntu4) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:s390x (8.2-4build1) ... Setting up libgcc-13-dev:s390x (13.2.0-23ubuntu4) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:s390x (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:s390x (13.2.0-23ubuntu4) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.1build1) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.1build1) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:s390x (1.3.0-3build3) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:s390x (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:s390x (3.1-0ubuntu7) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15545 files and directories currently installed.) Purging configuration files for libssl3:s390x (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28273980 s390x noble -c chroot:build-PACKAGEBUILD-28273980 --arch=s390x --dist=noble --nolog unifrac-tools_1.4-3build2.dsc Initiating build PACKAGEBUILD-28273980 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-181-generic #201-Ubuntu SMP Thu Mar 28 15:39:22 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-s390x-004.buildd +==============================================================================+ | unifrac-tools 1.4-3build2 (s390x) Tue, 14 May 2024 07:16:50 +0000 | +==============================================================================+ Package: unifrac-tools Version: 1.4-3build2 Source Version: 1.4-3build2 Distribution: noble Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28273980/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/unifrac-tools-4e4I3c/resolver-nuYWer' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- unifrac-tools_1.4-3build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/unifrac-tools-4e4I3c/unifrac-tools-1.4' with '<>' I: NOTICE: Log filtering will replace 'build/unifrac-tools-4e4I3c' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, libhdf5-dev, hdf5-helpers, liblz4-dev, libblas-dev, liblapacke-dev, chrpath, gfortran, python3, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-exec, libhdf5-dev, hdf5-helpers, liblz4-dev, libblas-dev, liblapacke-dev, chrpath, gfortran, python3, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [434 B] Get:5 copy:/<>/apt_archive ./ Packages [508 B] Fetched 1899 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev chrpath debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-s390x-linux-gnu gfortran-s390x-linux-gnu groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libblas-dev libblas3 libbrotli1 libcurl4-openssl-dev libcurl4t64 libdebhelper-perl libdw1t64 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblapacke liblapacke-dev libldap2 liblz4-dev libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db media-types netbase po-debconf python3 python3-minimal python3.12 python3.12-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev groff liblapack-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config libhdf5-doc libssl-doc libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev chrpath debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-s390x-linux-gnu gfortran-s390x-linux-gnu groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libblas-dev libblas3 libbrotli1 libcurl4-openssl-dev libcurl4t64 libdebhelper-perl libdw1t64 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblapacke liblapacke-dev libldap2 liblz4-dev libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db media-types netbase po-debconf python3 python3-minimal python3.12 python3.12-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 57.8 MB of archives. After this operation, 218 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [728 B] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libpython3.12-minimal s390x 3.12.3-1 [830 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libexpat1 s390x 2.6.1-2build1 [94.4 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main s390x python3.12-minimal s390x 3.12.3-1 [2460 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x python3-minimal s390x 3.12.3-0ubuntu1 [27.2 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x netbase all 6.4 [13.1 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libpython3.12-stdlib s390x 3.12.3-1 [2066 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x python3.12 s390x 3.12.3-1 [651 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libpython3-stdlib s390x 3.12.3-0ubuntu1 [9898 B] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x python3 s390x 3.12.3-0ubuntu1 [24.1 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libelf1t64 s390x 0.190-1.1build4 [69.7 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libicu74 s390x 74.2-1ubuntu3 [10.9 MB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu3 [818 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libmagic-mgc s390x 1:5.45-3build1 [305 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libmagic1t64 s390x 1:5.45-3build1 [93.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x file s390x 1:5.45-3build1 [22.2 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x gettext-base s390x 0.21-14ubuntu2 [39.4 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libuchardet0 s390x 0.0.8-1build1 [76.7 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x groff-base s390x 1.23.0-3build2 [1049 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main 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hdf5-helpers s390x 1.10.10+repack-3.1ubuntu4 [15.8 kB] Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x libaec0 s390x 1.1.2-1build1 [26.1 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libblas-dev s390x 3.12.0-3build1 [239 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libbrotli1 s390x 1.1.0-2build2 [375 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-5ubuntu3 [21.3 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main s390x libsasl2-2 s390x 2.1.28+dfsg1-5ubuntu3 [57.8 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main s390x libldap2 s390x 2.6.7+dfsg-1~exp1ubuntu8 [203 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build7 [58.4 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libssh-4 s390x 0.10.6-2build2 [189 kB] Get:61 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s390x 1.10.10+repack-3.1ubuntu4 [11.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3.1ubuntu2 [904 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8-dev s390x 2.1.5-2ubuntu2 [284 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] Get:76 http://ftpmaster.internal/ubuntu noble/universe s390x libaec-dev s390x 1.1.2-1build1 [23.5 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x libssl-dev s390x 3.0.13-0ubuntu3 [2131 kB] Get:78 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-dev s390x 1.10.10+repack-3.1ubuntu4 [2908 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x liblapack-dev s390x 3.12.0-3build1 [5983 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x libtmglib3 s390x 3.12.0-3build1 [153 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x liblapacke s390x 3.12.0-3build1 [437 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main s390x libtmglib-dev s390x 3.12.0-3build1 [154 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x liblapacke-dev s390x 3.12.0-3build1 [367 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x dh-exec s390x 0.29build1 [25.9 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x liblz4-dev s390x 1.9.4-1build1 [107 kB] Preconfiguring packages ... Fetched 57.8 MB in 8s (7338 kB/s) Selecting previously unselected package libpython3.12-minimal:s390x. (Reading database ... 15545 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.3-1_s390x.deb ... Unpacking libpython3.12-minimal:s390x (3.12.3-1) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.6.1-2build1_s390x.deb ... Unpacking libexpat1:s390x (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.3-1_s390x.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Setting up libpython3.12-minimal:s390x (3.12.3-1) ... Setting up libexpat1:s390x (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 15863 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu1_s390x.deb ... 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Setting up libblas3:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libssl-dev:s390x (3.0.13-0ubuntu3) ... Setting up autopoint (0.21-14ubuntu2) ... Setting up liblz4-dev:s390x (1.9.4-1build1) ... Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... Setting up libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu3) ... Setting up libssh-4:s390x (0.10.6-2build2) ... Setting up libgfortran5:s390x (14-20240412-0ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libicu74:s390x (74.2-1ubuntu3) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libuchardet0:s390x (0.0.8-1build1) ... Setting up debugedit (1:5.0-5build2) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... 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Setting up liblapacke:s390x (3.12.0-3build1) ... Setting up gfortran-13-s390x-linux-gnu (13.2.0-23ubuntu4) ... Setting up libtmglib-dev:s390x (3.12.0-3build1) ... Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... Setting up libhdf5-103-1t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libpython3-stdlib:s390x (3.12.3-0ubuntu1) ... Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up gfortran-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhdf5-cpp-103-1t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... Setting up libhdf5-fortran-102t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up python3 (3.12.3-0ubuntu1) ... Setting up liblapacke-dev:s390x (3.12.0-3build1) ... Setting up man-db (2.12.0-4build2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up gfortran-13 (13.2.0-23ubuntu4) ... Setting up libhdf5-hl-cpp-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libhdf5-hl-fortran-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up dh-exec (0.29build1) ... Setting up gfortran (4:13.2.0-7ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist Setting up libhdf5-dev (1.10.10+repack-3.1ubuntu4) ... update-alternatives: using /usr/lib/s390x-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/s390x-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.4-1ubuntu8) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-181-generic #201-Ubuntu SMP Thu Mar 28 15:39:22 UTC 2024 s390x (s390x) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: unifrac-tools Binary: unifrac-tools, libssu0, libssu-dev Architecture: any Version: 1.4-3build2 Maintainer: Ubuntu Developers Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/biocore/unifrac-binaries Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/unifrac-tools Vcs-Git: https://salsa.debian.org/med-team/unifrac-tools.git Testsuite: autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), dh-exec, libhdf5-dev, hdf5-helpers, liblz4-dev, libblas-dev, liblapacke-dev, chrpath, gfortran, python3 Package-List: libssu-dev deb libdevel optional arch=any libssu0 deb libs optional arch=any unifrac-tools deb science optional arch=any Checksums-Sha1: 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dpkg-source: info: applying remove_non-free_headers.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying soname.patch dpkg-source: info: applying baseline.patch dpkg-source: info: applying enable_linking_to_shared_hdf5_lib.patch dpkg-source: info: applying enable-debug-flag.patch dpkg-source: info: applying hardening dpkg-source: info: applying PR53.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-28273980 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28273980 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28273980 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package unifrac-tools dpkg-buildpackage: info: source version 1.4-3build2 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/<>' cd test && make clean make[2]: Entering directory '/<>/test' rm -f *.o capi_test make[2]: Leaving directory '/<>/test' cd src && make clean make[2]: Entering directory '/<>/src' rm -f *.o ssu faithpd test_su test_ska test_api libssu.so make[2]: Leaving directory '/<>/src' cd combined && make clean make[2]: Entering directory '/<>/combined' rm -f libssu.o libssu.so make[2]: Leaving directory '/<>/combined' make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -O--no-parallel dh_auto_configure -a -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p /<>/debian/tmp/usr/bin mkdir -p /<>/debian/tmp/usr/lib dh_auto_build -- PREFIX=/<>/debian/tmp/usr make -j1 "INSTALL=install --strip-program=true" PREFIX=/<>/debian/tmp/usr make[2]: Entering directory '/<>' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make clean && make api make[3]: Entering directory '/<>/src' rm -f *.o ssu_cpu_basic faithpd_cpu_basic test_su test_ska test_api libssu_cpu_basic.so make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c tree.cpp -o tree.o tree.cpp: In member function ‘su::BPTree::newick_to_bp(std::__cxx11::basic_string, std::allocator >)’: tree.cpp:321:48: warning: ‘last_structure’ may be used uninitialized [-Wmaybe-uninitialized] 321 | if(potential_single_descendent || (last_structure == ',')) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:300:10: note: ‘last_structure’ was declared here 300 | char last_structure; | ^~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:32:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:14, from biom.cpp:13: /usr/include/hdf5/serial/H5File.h:104:5: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 104 | 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:24:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 24 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:46: /usr/include/hdf5/serial/H5Group.h:62:5: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 62 | Group(const Group &original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:32:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:134:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 135 | 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:166:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(const std::string&, uint32_t*&, double*&)’: biom.cpp:206:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:212:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(const std::string&, uint32_t*&, double*&)’: biom.cpp:251:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:257:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o biom_inmem.cpp: In constructor ‘su::biom_inmem::biom_inmem(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int)’: biom_inmem.cpp:328:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 328 | for(int i = 0; i < n_obs; i++) { | ~~^~~~~~~ biom_inmem.cpp:333:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 333 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ biom_inmem.cpp: In instantiation of ‘void su::biom_inmem::get_obs_data_range_TT(uint32_t, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; uint32_t = unsigned int]’: biom_inmem.cpp:427:34: required from ‘void su::biom_inmem::get_obs_data_range_TT(const std::string&, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; std::string = std::__cxx11::basic_string]’ biom_inmem.cpp:431:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘unsigned int’ [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j]’ biom_inmem.cpp:435:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘unsigned int’ [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom_subsampled.cpp -o biom_subsampled.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c tsv.cpp -o tsv.o tsv.cpp: In member function ‘void su::indexed_tsv::read_grouping(const std::string&, uint32_t*, uint32_t&) const’: tsv.cpp:126:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 126 | for (int i=1; i< header_line.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~~ tsv.cpp:138:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 138 | for (int i=1; i< n_filter_els; i++) grouping[i] = n_filter_els; | ~^~~~~~~~~~~~~~ tsv.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 173 | for (int i=1; i< n_filter_els; i++) { | ~^~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:13: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: ‘int bind_to_core(int)’ defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c cmd.cpp -o cmd.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status one_off_inmem_cpp(su::biom_interface&, su::BPTree&, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:443:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 443 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld 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:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:97:62: note: in expansion of macro ‘PARSE_TREE_TABLE’ 97 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ | ^~~~~~~~~~~~~~~~ api.cpp:474:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 474 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:485:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 485 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:513:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 513 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:550:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 550 | PARSE_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off_matrix_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp64_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:628:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 628 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off_matrix_fp32_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp32_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:650:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 650 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘IOStatus read_partial_header_fd(int, TPMat&)’: api.cpp:1795:83: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp: In instantiation of ‘compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = double; TMat = mat_full_fp64; hid_t = long int]’: api.cpp:1400:59: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = float; TMat = mat_full_fp32; hid_t = long int]’: api.cpp:1408:58: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]’: api.cpp:1963:48: required from here api.cpp:1795:83: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:1821:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1821 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1827:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1827 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} | ~~~^~~~~~~~~~~~~~~~~~ api.cpp:1831:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1831 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp: In instantiation of ‘IOStatus read_partial_data_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]’: api.cpp:1965:49: required from here api.cpp:1864:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1864 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:1868:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1868 | if ( (i+1)n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]’: api.cpp:2109:36: required from here api.cpp:2042:39: warning: comparison of integer expressions of different signedness: ‘const uint32_t’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare] 2042 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = double; TMat = mat_full_fp64]’: api.cpp:257:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 257 | ftruncate(fd,msize); | ~~~~~~~~~^~~~~~~~~~ api.cpp: In function ‘void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = float; TMat = mat_full_fp32]’: api.cpp:257:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o In file included from unifrac_internal.cpp:12: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: ‘int bind_to_core(int)’ defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o In file included from unifrac_cmp.cpp:19: unifrac_task.hpp:196: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 196 | #pragma acc enter data create(buf[:bsize]) | unifrac_task.hpp:357: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 357 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:395: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 395 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:438: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 438 | #pragma acc enter data create(zcheck[:n_samples],stripe_sums[:n_samples],sums[:bsize]) | In file included from unifrac_cmp.cpp:24: unifrac_task.cpp:41: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 41 | #pragma acc loop seq | unifrac_task.cpp:558: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 558 | #pragma acc loop seq | unifrac_task.cpp:1008: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1008 | #pragma acc loop seq | unifrac_task.cpp:1081: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1081 | #pragma acc loop seq | unifrac_task.cpp:1159: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1159 | #pragma acc loop seq | unifrac_task.cpp:1544: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1544 | #pragma acc loop vector | unifrac_task.cpp:1573: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1573 | #pragma acc loop vector | unifrac_task.cpp:1586: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 1586 | #pragma acc wait | unifrac_task.cpp:1700: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1700 | #pragma acc loop seq | unifrac_task.cpp:1710: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1710 | #pragma acc loop seq | unifrac_cmp.cpp:97: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 97 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:195: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 195 | #pragma acc wait | unifrac_cmp.cpp:204: warning: ignoring ‘#pragma acc parallel’ [-Wunknown-pragmas] 204 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:214: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 214 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:282: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 282 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp:293: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 293 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:338: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 338 | #pragma acc wait | unifrac_cmp.cpp:339: warning: ignoring ‘#pragma acc update’ [-Wunknown-pragmas] 339 | #pragma acc update device(lengths[:filled_emb]) | unifrac_cmp.cpp:347: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 347 | #pragma acc wait | unifrac_cmp.cpp:355: warning: ignoring ‘#pragma acc parallel’ [-Wunknown-pragmas] 355 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:366: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 366 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:367: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 367 | #pragma acc exit data delete(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = double]’: unifrac_cmp.cpp:226:70: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:229:78: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:232:80: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = double]’: unifrac_cmp.cpp:235:71: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = float]’: unifrac_cmp.cpp:238:69: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:241:77: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:244:79: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = float]’: unifrac_cmp.cpp:247:70: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]’: unifrac_cmp.cpp:380:77: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:383:85: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:386:87: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = double]’: unifrac_cmp.cpp:389:78: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]’: unifrac_cmp.cpp:392:77: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:395:85: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:398:87: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = float]’: unifrac_cmp.cpp:401:78: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:435:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:393:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:355:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:435:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:393:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:355:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5c++ -shared -fopenmp -shlib -o libssu_cpu_basic.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu_cpu_basic.so.0 -llapacke -lblas -lgfortran -L/<>/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 ln -sf libssu_cpu_basic.so.0 libssu_cpu_basic.so # FIXME: Should build static lib as well # h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/<>/debian/tmp/usr/lib make[3]: Leaving directory '/<>/src' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib su.cpp -o ssu_cpu_basic tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib faithpd.cpp -o faithpd_cpu_basic tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread make[3]: Leaving directory '/<>/src' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install make[3]: Entering directory '/<>/src' rm -f /<>/debian/tmp/usr/lib//libssu_cpu_basic.so; cp -a libssu_cpu_basic.so* /<>/debian/tmp/usr/lib/ rm -f /<>/debian/tmp/usr/bin/ssu_cpu_basic; cp ssu_cpu_basic /<>/debian/tmp/usr/bin/ rm -f /<>/debian/tmp/usr/bin/faithpd_cpu_basic; cp faithpd_cpu_basic /<>/debian/tmp/usr/bin/ mkdir -p /<>/debian/tmp/usr/include/unifrac rm -f /<>/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /<>/debian/tmp/usr/include/unifrac/ rm -f /<>/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /<>/debian/tmp/usr/include/unifrac/ rm -f /<>/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /<>/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/<>/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make clean && make api /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' rm -f *.o ssu_nv_avx2 faithpd_nv_avx2 test_su test_ska test_api libssu_nv_avx2.so make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c tree.cpp -o tree.o tree.cpp: In member function ‘su::BPTree::newick_to_bp(std::__cxx11::basic_string, std::allocator >)’: tree.cpp:321:48: warning: ‘last_structure’ may be used uninitialized [-Wmaybe-uninitialized] 321 | if(potential_single_descendent || (last_structure == ',')) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:300:10: note: ‘last_structure’ was declared here 300 | char last_structure; | ^~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:32:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:14, from biom.cpp:13: /usr/include/hdf5/serial/H5File.h:104:5: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 104 | 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:24:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 24 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:46: /usr/include/hdf5/serial/H5Group.h:62:5: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 62 | Group(const Group &original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:32:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:134:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 135 | 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:166:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(const std::string&, uint32_t*&, double*&)’: biom.cpp:206:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:212:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(const std::string&, uint32_t*&, double*&)’: biom.cpp:251:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:257:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o biom_inmem.cpp: In constructor ‘su::biom_inmem::biom_inmem(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int)’: biom_inmem.cpp:328:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 328 | for(int i = 0; i < n_obs; i++) { | ~~^~~~~~~ biom_inmem.cpp:333:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 333 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ biom_inmem.cpp: In instantiation of ‘void su::biom_inmem::get_obs_data_range_TT(uint32_t, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; uint32_t = unsigned int]’: biom_inmem.cpp:427:34: required from ‘void su::biom_inmem::get_obs_data_range_TT(const std::string&, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; std::string = std::__cxx11::basic_string]’ biom_inmem.cpp:431:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘unsigned int’ [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j]’ biom_inmem.cpp:435:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘unsigned int’ [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom_subsampled.cpp -o biom_subsampled.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c tsv.cpp -o tsv.o tsv.cpp: In member function ‘void su::indexed_tsv::read_grouping(const std::string&, uint32_t*, uint32_t&) const’: tsv.cpp:126:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 126 | for (int i=1; i< header_line.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~~ tsv.cpp:138:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 138 | for (int i=1; i< n_filter_els; i++) grouping[i] = n_filter_els; | ~^~~~~~~~~~~~~~ tsv.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 173 | for (int i=1; i< n_filter_els; i++) { | ~^~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:13: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: ‘int bind_to_core(int)’ defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c cmd.cpp -o cmd.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status one_off_inmem_cpp(su::biom_interface&, su::BPTree&, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:443:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 443 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld 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:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:97:62: note: in expansion of macro ‘PARSE_TREE_TABLE’ 97 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ | ^~~~~~~~~~~~~~~~ api.cpp:474:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 474 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:485:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 485 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:513:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 513 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:550:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 550 | PARSE_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off_matrix_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp64_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:628:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 628 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off_matrix_fp32_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp32_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:650:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 650 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘IOStatus read_partial_header_fd(int, TPMat&)’: api.cpp:1795:83: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp: In instantiation of ‘compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = double; TMat = mat_full_fp64; hid_t = long int]’: api.cpp:1400:59: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = float; TMat = mat_full_fp32; hid_t = long int]’: api.cpp:1408:58: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]’: api.cpp:1963:48: required from here api.cpp:1795:83: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:1821:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1821 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1827:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1827 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} | ~~~^~~~~~~~~~~~~~~~~~ api.cpp:1831:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1831 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp: In instantiation of ‘IOStatus read_partial_data_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]’: api.cpp:1965:49: required from here api.cpp:1864:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1864 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:1868:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1868 | if ( (i+1)n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]’: api.cpp:2109:36: required from here api.cpp:2042:39: warning: comparison of integer expressions of different signedness: ‘const uint32_t’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare] 2042 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = double; TMat = mat_full_fp64]’: api.cpp:257:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 257 | ftruncate(fd,msize); | ~~~~~~~~~^~~~~~~~~~ api.cpp: In function ‘void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = float; TMat = mat_full_fp32]’: api.cpp:257:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o In file included from unifrac_internal.cpp:12: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: ‘int bind_to_core(int)’ defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o In file included from unifrac_cmp.cpp:19: unifrac_task.hpp:196: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 196 | #pragma acc enter data create(buf[:bsize]) | unifrac_task.hpp:357: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 357 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:395: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 395 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:438: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 438 | #pragma acc enter data create(zcheck[:n_samples],stripe_sums[:n_samples],sums[:bsize]) | In file included from unifrac_cmp.cpp:24: unifrac_task.cpp:41: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 41 | #pragma acc loop seq | unifrac_task.cpp:558: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 558 | #pragma acc loop seq | unifrac_task.cpp:1008: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1008 | #pragma acc loop seq | unifrac_task.cpp:1081: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1081 | #pragma acc loop seq | unifrac_task.cpp:1159: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1159 | #pragma acc loop seq | unifrac_task.cpp:1544: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1544 | #pragma acc loop vector | unifrac_task.cpp:1573: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1573 | #pragma acc loop vector | unifrac_task.cpp:1586: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 1586 | #pragma acc wait | unifrac_task.cpp:1700: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1700 | #pragma acc loop seq | unifrac_task.cpp:1710: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1710 | #pragma acc loop seq | unifrac_cmp.cpp:97: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 97 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:195: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 195 | #pragma acc wait | unifrac_cmp.cpp:204: warning: ignoring ‘#pragma acc parallel’ [-Wunknown-pragmas] 204 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:214: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 214 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:282: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 282 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp:293: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 293 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:338: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 338 | #pragma acc wait | unifrac_cmp.cpp:339: warning: ignoring ‘#pragma acc update’ [-Wunknown-pragmas] 339 | #pragma acc update device(lengths[:filled_emb]) | unifrac_cmp.cpp:347: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 347 | #pragma acc wait | unifrac_cmp.cpp:355: warning: ignoring ‘#pragma acc parallel’ [-Wunknown-pragmas] 355 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:366: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 366 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:367: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 367 | #pragma acc exit data delete(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = double]’: unifrac_cmp.cpp:226:70: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:229:78: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:232:80: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = double]’: unifrac_cmp.cpp:235:71: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = float]’: unifrac_cmp.cpp:238:69: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:241:77: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:244:79: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = float]’: unifrac_cmp.cpp:247:70: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]’: unifrac_cmp.cpp:380:77: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:383:85: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:386:87: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = double]’: unifrac_cmp.cpp:389:78: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]’: unifrac_cmp.cpp:392:77: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:395:85: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:398:87: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = float]’: unifrac_cmp.cpp:401:78: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:435:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:393:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:355:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:435:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:393:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:355:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5c++ -shared -fopenmp -shlib -o libssu_nv_avx2.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu_nv_avx2.so.0 -llapacke -lblas -lgfortran -L/<>/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 ln -sf libssu_nv_avx2.so.0 libssu_nv_avx2.so # FIXME: Should build static lib as well # h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/<>/debian/tmp/usr/lib make[3]: Leaving directory '/<>/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make main /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib su.cpp -o ssu_nv_avx2 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib faithpd.cpp -o faithpd_nv_avx2 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread make[3]: Leaving directory '/<>/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make install /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' rm -f /<>/debian/tmp/usr/lib//libssu_nv_avx2.so; cp -a libssu_nv_avx2.so* /<>/debian/tmp/usr/lib/ rm -f /<>/debian/tmp/usr/bin/ssu_nv_avx2; cp ssu_nv_avx2 /<>/debian/tmp/usr/bin/ rm -f /<>/debian/tmp/usr/bin/faithpd_nv_avx2; cp faithpd_nv_avx2 /<>/debian/tmp/usr/bin/ mkdir -p /<>/debian/tmp/usr/include/unifrac rm -f /<>/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /<>/debian/tmp/usr/include/unifrac/ rm -f /<>/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /<>/debian/tmp/usr/include/unifrac/ rm -f /<>/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /<>/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/<>/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make clean && make api /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' rm -f *.o ssu_nv faithpd_nv test_su test_ska test_api libssu_nv.so make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c tree.cpp -o tree.o tree.cpp: In member function ‘su::BPTree::newick_to_bp(std::__cxx11::basic_string, std::allocator >)’: tree.cpp:321:48: warning: ‘last_structure’ may be used uninitialized [-Wmaybe-uninitialized] 321 | if(potential_single_descendent || (last_structure == ',')) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:300:10: note: ‘last_structure’ was declared here 300 | char last_structure; | ^~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:32:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:14, from biom.cpp:13: /usr/include/hdf5/serial/H5File.h:104:5: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 104 | 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:24:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 24 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:46: /usr/include/hdf5/serial/H5Group.h:62:5: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 62 | Group(const Group &original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:32:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:134:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 135 | 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:166:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(const std::string&, uint32_t*&, double*&)’: biom.cpp:206:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:212:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(const std::string&, uint32_t*&, double*&)’: biom.cpp:251:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:257:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o biom_inmem.cpp: In constructor ‘su::biom_inmem::biom_inmem(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int)’: biom_inmem.cpp:328:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 328 | for(int i = 0; i < n_obs; i++) { | ~~^~~~~~~ biom_inmem.cpp:333:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 333 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ biom_inmem.cpp: In instantiation of ‘void su::biom_inmem::get_obs_data_range_TT(uint32_t, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; uint32_t = unsigned int]’: biom_inmem.cpp:427:34: required from ‘void su::biom_inmem::get_obs_data_range_TT(const std::string&, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; std::string = std::__cxx11::basic_string]’ biom_inmem.cpp:431:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘unsigned int’ [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j]’ biom_inmem.cpp:435:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘unsigned int’ [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c biom_subsampled.cpp -o biom_subsampled.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c tsv.cpp -o tsv.o tsv.cpp: In member function ‘void su::indexed_tsv::read_grouping(const std::string&, uint32_t*, uint32_t&) const’: tsv.cpp:126:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 126 | for (int i=1; i< header_line.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~~ tsv.cpp:138:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 138 | for (int i=1; i< n_filter_els; i++) grouping[i] = n_filter_els; | ~^~~~~~~~~~~~~~ tsv.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 173 | for (int i=1; i< n_filter_els; i++) { | ~^~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:13: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: ‘int bind_to_core(int)’ defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c cmd.cpp -o cmd.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status one_off_inmem_cpp(su::biom_interface&, su::BPTree&, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:443:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 443 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld 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:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:97:62: note: in expansion of macro ‘PARSE_TREE_TABLE’ 97 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ | ^~~~~~~~~~~~~~~~ api.cpp:474:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 474 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:485:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 485 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:513:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 513 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:550:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 550 | PARSE_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off_matrix_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp64_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:628:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 628 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off_matrix_fp32_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp32_t**)’: api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:650:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 650 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function ‘IOStatus read_partial_header_fd(int, TPMat&)’: api.cpp:1795:83: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp: In instantiation of ‘compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = double; TMat = mat_full_fp64; hid_t = long int]’: api.cpp:1400:59: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = float; TMat = mat_full_fp32; hid_t = long int]’: api.cpp:1408:58: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro ‘PARSE_TREE_TABLE’ 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]’: api.cpp:1963:48: required from here api.cpp:1795:83: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:1821:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1821 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1827:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1827 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} | ~~~^~~~~~~~~~~~~~~~~~ api.cpp:1831:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1831 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp: In instantiation of ‘IOStatus read_partial_data_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]’: api.cpp:1965:49: required from here api.cpp:1864:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1864 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:1868:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 1868 | if ( (i+1)n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In instantiation of ‘MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]’: api.cpp:2109:36: required from here api.cpp:2042:39: warning: comparison of integer expressions of different signedness: ‘const uint32_t’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare] 2042 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = double; TMat = mat_full_fp64]’: api.cpp:257:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 257 | ftruncate(fd,msize); | ~~~~~~~~~^~~~~~~~~~ api.cpp: In function ‘void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = float; TMat = mat_full_fp32]’: api.cpp:257:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o In file included from unifrac_internal.cpp:12: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: ‘int bind_to_core(int)’ defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o In file included from unifrac_cmp.cpp:19: unifrac_task.hpp:196: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 196 | #pragma acc enter data create(buf[:bsize]) | unifrac_task.hpp:357: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 357 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:395: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 395 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:438: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 438 | #pragma acc enter data create(zcheck[:n_samples],stripe_sums[:n_samples],sums[:bsize]) | In file included from unifrac_cmp.cpp:24: unifrac_task.cpp:41: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 41 | #pragma acc loop seq | unifrac_task.cpp:558: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 558 | #pragma acc loop seq | unifrac_task.cpp:1008: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1008 | #pragma acc loop seq | unifrac_task.cpp:1081: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1081 | #pragma acc loop seq | unifrac_task.cpp:1159: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1159 | #pragma acc loop seq | unifrac_task.cpp:1544: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1544 | #pragma acc loop vector | unifrac_task.cpp:1573: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1573 | #pragma acc loop vector | unifrac_task.cpp:1586: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 1586 | #pragma acc wait | unifrac_task.cpp:1700: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1700 | #pragma acc loop seq | unifrac_task.cpp:1710: warning: ignoring ‘#pragma acc loop’ [-Wunknown-pragmas] 1710 | #pragma acc loop seq | unifrac_cmp.cpp:97: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 97 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:195: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 195 | #pragma acc wait | unifrac_cmp.cpp:204: warning: ignoring ‘#pragma acc parallel’ [-Wunknown-pragmas] 204 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:214: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 214 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:282: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 282 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp:293: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 293 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:338: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 338 | #pragma acc wait | unifrac_cmp.cpp:339: warning: ignoring ‘#pragma acc update’ [-Wunknown-pragmas] 339 | #pragma acc update device(lengths[:filled_emb]) | unifrac_cmp.cpp:347: warning: ignoring ‘#pragma acc wait’ [-Wunknown-pragmas] 347 | #pragma acc wait | unifrac_cmp.cpp:355: warning: ignoring ‘#pragma acc parallel’ [-Wunknown-pragmas] 355 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:366: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 366 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:367: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 367 | #pragma acc exit data delete(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = double]’: unifrac_cmp.cpp:226:70: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:229:78: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:232:80: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = double]’: unifrac_cmp.cpp:235:71: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = float]’: unifrac_cmp.cpp:238:69: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:241:77: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:244:79: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = float]’: unifrac_cmp.cpp:247:70: required from here unifrac_cmp.cpp:94:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]’: unifrac_cmp.cpp:380:77: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:383:85: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = double]’: unifrac_cmp.cpp:386:87: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = double]’: unifrac_cmp.cpp:389:78: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]’: unifrac_cmp.cpp:392:77: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:395:85: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = float]’: unifrac_cmp.cpp:398:87: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of ‘void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = float]’: unifrac_cmp.cpp:401:78: required from here unifrac_cmp.cpp:290:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:435:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:393:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]’: unifrac_task.hpp:355:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:435:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:393:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor ‘su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]’: unifrac_task.hpp:355:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of ‘int posix_memalign(void**, size_t, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5c++ -shared -fopenmp -shlib -o libssu_nv.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu_nv.so.0 -llapacke -lblas -lgfortran -L/<>/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 ln -sf libssu_nv.so.0 libssu_nv.so # FIXME: Should build static lib as well # h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/<>/debian/tmp/usr/lib make[3]: Leaving directory '/<>/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib su.cpp -o ssu_nv tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib faithpd.cpp -o faithpd_nv tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread make[3]: Leaving directory '/<>/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' rm -f /<>/debian/tmp/usr/lib//libssu_nv.so; cp -a libssu_nv.so* /<>/debian/tmp/usr/lib/ rm -f /<>/debian/tmp/usr/bin/ssu_nv; cp ssu_nv /<>/debian/tmp/usr/bin/ rm -f /<>/debian/tmp/usr/bin/faithpd_nv; cp faithpd_nv /<>/debian/tmp/usr/bin/ mkdir -p /<>/debian/tmp/usr/include/unifrac rm -f /<>/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /<>/debian/tmp/usr/include/unifrac/ rm -f /<>/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /<>/debian/tmp/usr/include/unifrac/ rm -f /<>/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /<>/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/<>/src' cd combined && make api make[3]: Entering directory '/<>/combined' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -c libssu.c -fPIC cc -shared -o libssu.so libssu.o -fPIC -ldl -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/combined' cd combined && make install make[3]: Entering directory '/<>/combined' rm -f /<>/debian/tmp/usr/lib//libssu.so; cp libssu.so /<>/debian/tmp/usr/lib/ rm -f /<>/debian/tmp/usr/bin/ssu; cp ssu /<>/debian/tmp/usr/bin/ rm -f /<>/debian/tmp/usr/bin/faithpd; cp faithpd /<>/debian/tmp/usr/bin/ make[3]: Leaving directory '/<>/combined' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make test_binaries /bin/sh: 1: source: not found make[3]: Entering directory '/<>/src' h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib test_su.cpp -o test_su tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o skbio_alt.o api.o -llz4 -llapacke -lblas -lgfortran -lpthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:302:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 302 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:320:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 320 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:340:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 340 | uint32_t obs[tree.nparens - 2]; | ^~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib test_ska.cpp -o test_ska skbio_alt.o tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o api.o -llz4 -llapacke -lblas -lgfortran -lpthread test_ska.cpp: In function ‘void test_pcoa_big()’: test_ska.cpp:271:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 271 | fscanf(fptr,"# unifrac %u\n",&n_samples); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test_ska.cpp:278:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 278 | fscanf(fptr,"%lf\n",&(matrix[i])); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ test_ska.cpp:281:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 281 | fscanf(fptr,"# pcoa %u\n",&n_dims); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ test_ska.cpp:286:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 286 | fscanf(fptr,"%lf\n",&(exp1[i])); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ test_ska.cpp:290:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 290 | fscanf(fptr,"%lf\n",&(exp2[i])); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ test_ska.cpp:294:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 294 | fscanf(fptr,"%lf\n",&(exp3[i])); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ h5c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/<>/debian/tmp/usr/lib test_api.cpp -o test_api tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o skbio_alt.o api.o -llz4 -llapacke -lblas -lgfortran -lpthread make[3]: Leaving directory '/<>/src' # use the default compiler for the test subdir as it tests the combined shlib cd test && make test_binaries make[3]: Entering directory '/<>/test' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/unifrac-tools-1.4-3build2 -std=c99 -O0 -g capi_test.c -I../src -lssu -L/<>/debian/tmp/usr/lib -Wl,-rpath,/<>/debian/tmp/usr/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o capi_test make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>' chmod +x /<>/debian/tmp/usr/bin/* make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/<>/debian/tmp/usr/bin ; \ cd ci ; \ ./crawford_test.sh HDF5-DIAG: Error detected in HDF5 (1.10.10) thread 1: #000: ../../../src/H5Dio.c line 172 in H5Dread(): could not get a validated dataspace from file_space_id major: Invalid arguments to routine minor: Bad value #001: ../../../src/H5S.c line 242 in H5S_get_validated_dataspace(): selection + offset not within extent major: Dataspace minor: Out of range terminate called after throwing an instance of 'H5::DataSetIException' ./crawford_test.sh: line 12: 13531 Aborted (core dumped) ssu -i crawford.biom -t crawford.tre -o test.dm -m unweighted make[1]: *** [debian/rules:20: override_dh_auto_test] Error 134 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-05-14T07:20:31Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 200908 Build-Time: 203 Distribution: noble Fail-Stage: build Host Architecture: s390x Install-Time: 18 Job: unifrac-tools_1.4-3build2.dsc Machine Architecture: s390x Package: unifrac-tools Package-Time: 221 Source-Version: 1.4-3build2 Space: 200908 Status: attempted Version: 1.4-3build2 -------------------------------------------------------------------------------- Finished at 2024-05-14T07:20:31Z Build needed 00:03:41, 200908k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28273980 Scanning for processes to kill in build PACKAGEBUILD-28273980