I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 8 08:17:38 +14 2025 I: pbuilder-time-stamp: 1736273858 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [unifrac-tools_1.4-3.dsc] I: copying [./unifrac-tools_1.4.orig.tar.gz] I: copying [./unifrac-tools_1.4-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./unifrac-tools_1.4-3.dsc: unsupported subcommand dpkg-source: info: extracting unifrac-tools in unifrac-tools-1.4 dpkg-source: info: unpacking unifrac-tools_1.4.orig.tar.gz dpkg-source: info: unpacking unifrac-tools_1.4-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/388004/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 7 18:17 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/388004/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/388004/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8f6fa85d96ff4b16aade2fca74e63b1a LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=388004 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ORl3sjci/pbuilderrc_AaVP --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ORl3sjci/b2 --logfile b2/build.log unifrac-tools_1.4-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/388004/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-exec, libhdf5-dev, hdf5-helpers, liblz4-dev, libblas-dev, liblapacke-dev, chrpath, gfortran, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on hdf5-helpers; however: Package hdf5-helpers is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapacke-dev; however: Package liblapacke-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} chrpath{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libldap-2.5-0{a} libldap-dev{a} liblz4-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libxxhash-dev{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 65.0 MB of archives. After unpacking 272 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-1 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-1 [9912 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-1 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-13 [91.4 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.23 [919 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B] Get: 54 http://deb.debian.org/debian unstable/main arm64 gfortran arm64 4:14.2.0-1 [1424 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 59 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.0-4 [106 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.19+dfsg-1 [175 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.1-1 [325 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.19+dfsg-1 [300 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libcurl4-openssl-dev arm64 8.11.1-1 [449 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.0-4 [3709 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libtmglib3 arm64 3.12.0-4 [98.6 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 liblapacke arm64 3.12.0-4 [337 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libtmglib-dev arm64 3.12.0-4 [103 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 liblapacke-dev arm64 3.12.0-4 [321 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libxxhash-dev arm64 0.8.3-2 [82.6 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 liblz4-dev arm64 1.9.4-4 [79.0 kB] Fetched 65.0 MB in 0s (156 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ... Unpacking python3.13 (3.13.1-3) ... 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Unpacking libgnutls28-dev:arm64 (3.8.8-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../089-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:arm64. Preparing to unpack .../090-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../091-libssl-dev_3.4.0-2_arm64.deb ... Unpacking libssl-dev:arm64 (3.4.0-2) ... Selecting previously unselected package libssh2-1-dev:arm64. Preparing to unpack .../092-libssh2-1-dev_1.11.1-1_arm64.deb ... Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:arm64. Preparing to unpack .../093-libzstd-dev_1.5.6+dfsg-2_arm64.deb ... Unpacking libzstd-dev:arm64 (1.5.6+dfsg-2) ... 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Selecting previously unselected package liblapacke-dev:arm64. Preparing to unpack .../110-liblapacke-dev_3.12.0-4_arm64.deb ... Unpacking liblapacke-dev:arm64 (3.12.0-4) ... Selecting previously unselected package libxxhash-dev:arm64. Preparing to unpack .../111-libxxhash-dev_0.8.3-2_arm64.deb ... Unpacking libxxhash-dev:arm64 (0.8.3-2) ... Selecting previously unselected package liblz4-dev:arm64. Preparing to unpack .../112-liblz4-dev_1.9.4-4_arm64.deb ... Unpacking liblz4-dev:arm64 (1.9.4-4) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.2-13) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up gettext-base (0.22.5-4) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:arm64 (1.1.3-1+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 7 18:18:19 UTC 2025. Universal Time is now: Tue Jan 7 18:18:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunbound8:arm64 (1.22.0-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3+b1) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.4.0-2) ... Setting up autopoint (0.22.5-4) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-12) ... Setting up autoconf (2.72-3) ... Setting up libxxhash-dev:arm64 (0.8.3-2) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up netbase (6.4) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.19.0-3+b3) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b6) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsz2:arm64 (1.1.3-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-12) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-4) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:arm64 (3.10-1+b1) ... Setting up libtool (2.5.4-2) ... Setting up libaec-dev:arm64 (1.1.3-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-3+b1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:arm64 (3.12.0-4) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up liblapack-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up liblz4-dev:arm64 (1.9.4-4) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up liblapacke:arm64 (3.12.0-4) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-12) ... Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libtmglib-dev:arm64 (3.12.0-4) ... Setting up gfortran-14 (14.2.0-12) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libpython3-stdlib:arm64 (3.13.1-1) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.8-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-1) ... Setting up liblapacke-dev:arm64 (3.12.0-4) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libldap-2.5-0:arm64 (2.5.19+dfsg-1) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.8-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-3) ... Setting up libldap-dev:arm64 (2.5.19+dfsg-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-3) ... Setting up libgnutls28-dev:arm64 (3.8.8-2) ... Setting up libcurl4t64:arm64 (8.11.1-1) ... Setting up libkdb5-10t64:arm64 (1.21.3-3) ... Setting up debhelper (13.23) ... Setting up dh-exec (0.30+b1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-3) ... Setting up libhdf5-fortran-310:arm64 (1.14.5+repack-3) ... Setting up krb5-multidev:arm64 (1.21.3-3) ... Setting up libhdf5-cpp-310:arm64 (1.14.5+repack-3) ... Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Setting up libkrb5-dev:arm64 (1.21.3-3) ... Setting up libcurl4-openssl-dev:arm64 (8.11.1-1) ... Setting up libhdf5-hl-cpp-310:arm64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:arm64 (1.14.5+repack-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.40-5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/388004/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/388004/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/unifrac-tools-1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../unifrac-tools_1.4-3_source.changes dpkg-buildpackage: info: source package unifrac-tools dpkg-buildpackage: info: source version 1.4-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' cd test && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/test' rm -f *.o capi_test make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/test' cd src && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f *.o ssu faithpd test_su test_ska test_api libssu.so make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' cd combined && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/combined' rm -f libssu.o libssu.so make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/combined' make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib dh_auto_build -- PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make clean && make api make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f *.o ssu_cpu_basic faithpd_cpu_basic test_su test_ska test_api libssu_cpu_basic.so make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c tree.cpp -o tree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ tree.cpp: In member function 'void su::BPTree::newick_to_bp(std::string)': tree.cpp:321:67: 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom.cpp -o biom.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:115:5: note: because 'H5::H5File' has user-provided 'H5::H5File::H5File(const H5::H5File&)' 115 | H5File(const H5File &original); | ^~~~~~ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 member function 'void su::biom_inmem::compute_sample_counts()': biom_inmem.cpp:439:37: warning: 'void* calloc(size_t, size_t)' sizes specified with 'sizeof' in the earlier argument and not in the later argument [-Wcalloc-transposed-args] 439 | sample_counts = (double*)calloc(sizeof(double), n_samples); | ^~~~~~~~~~~~~~ biom_inmem.cpp:439:37: note: earlier argument should specify number of elements, later size of each element 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]' 427 | get_obs_data_range_TT(idx,start,end,normalize,out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ biom_inmem.cpp:431:36: required from here 431 | biom_inmem::get_obs_data_range_TT(id,start,end,normalize,out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]' 427 | get_obs_data_range_TT(idx,start,end,normalize,out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ biom_inmem.cpp:435:36: required from here 435 | biom_inmem::get_obs_data_range_TT(id,start,end,normalize,out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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::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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from unifrac.cpp:13: affinity.hpp:1:9: 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c cmd.cpp -o cmd.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 1400 | rc = unifrac_multi_to_file_T(H5T_IEEE_F64LE, save_dist, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1401 | biom_filename, tree_filename, out_filename, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | unifrac_method, variance_adjust, alpha, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1403 | bypass_tips, nsubsteps, format, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1404 | n_subsamples, subsample_depth, subsample_with_replacement, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1405 | pcoa_dims, permanova_perms, grouping_filename, grouping_columns, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1406 | mmap_dir); | ~~~~~~~~~ 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 1408 | rc = unifrac_multi_to_file_T(H5T_IEEE_F32LE, save_dist, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1409 | biom_filename, tree_filename, out_filename, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | unifrac_method, variance_adjust, alpha, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1411 | bypass_tips, nsubsteps, format, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1412 | n_subsamples, subsample_depth, subsample_with_replacement, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1413 | pcoa_dims, permanova_perms, grouping_filename, grouping_columns, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1414 | mmap_dir); | ~~~~~~~~~ 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 1963 | sts = read_partial_header_fd(fd, *result); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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 1965 | sts = read_partial_data_fd(fd, *result); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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)(fd, *result); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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_one_stripe_fd(int, TPMat&, uint32_t) [with TPMat = partial_dyn_mat; IOStatus = io_status; uint32_t = unsigned int]': api.cpp:2022:65: required from here 2022 | IOStatus sts = read_partial_one_stripe_fd(fd, *result, stripe_idx); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1908:58: warning: comparison of integer expressions of different signedness: '__off_t' {aka 'long int'} and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] 1908 | if (lseek(fd, result.offsets[curr_idx], SEEK_SET)!=result.offsets[curr_idx]) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ api.cpp:1924:58: warning: comparison of integer expressions of different signedness: '__off_t' {aka 'long int'} and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] 1924 | if (lseek(fd, result.offsets[stripe_idx], SEEK_SET)!=result.offsets[stripe_idx]) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ api.cpp:1937:17: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1937 | if (cnt != read_size) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~ api.cpp:1945:17: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 1945 | if (cnt != ( sizeof(double) * n_samples ) ) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In instantiation of 'MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_dyn_mat; MergeStatus = merge_status]': api.cpp:2104:25: required from here 2104 | return check_partial(partial_mats, n_partials, true); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2038:38: warning: 'void* calloc(size_t, size_t)' sizes specified with 'sizeof' in the earlier argument and not in the later argument [-Wcalloc-transposed-args] 2038 | bool *stripe_map = (bool*)calloc(sizeof(bool), partial_mats[0]->stripe_total); | ^~~~~~~~~~~~ api.cpp:2038:38: note: earlier argument should specify number of elements, later size of each element 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 instantiation of 'MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]': api.cpp:2109:36: required from here 2109 | MergeStatus err = check_partial(partial_mats, n_partials, false); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2038:38: warning: 'void* calloc(size_t, size_t)' sizes specified with 'sizeof' in the earlier argument and not in the later argument [-Wcalloc-transposed-args] 2038 | bool *stripe_map = (bool*)calloc(sizeof(bool), partial_mats[0]->stripe_total); | ^~~~~~~~~~~~ api.cpp:2038:38: note: earlier argument should specify number of elements, later size of each element 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from unifrac_internal.cpp:12: affinity.hpp:1:9: 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; | ^~~ unifrac_internal.cpp: In function 'void su::register_report_status()': unifrac_internal.cpp:67:35: warning: 'void* calloc(size_t, size_t)' sizes specified with 'sizeof' in the earlier argument and not in the later argument [-Wcalloc-transposed-args] 67 | report_status = (bool*)calloc(sizeof(bool), CPU_SETSIZE); | ^~~~~~~~~~~~ unifrac_internal.cpp:67:35: note: earlier argument should specify number of elements, later size of each element 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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_task.hpp:90:32: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 90 | UnifracTaskVector(const UnifracTaskVector& ) = delete; | ^ unifrac_task.hpp:90:32: note: remove the '< >' unifrac_task.hpp:156:37: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 156 | UnifracTaskBase(const UnifracTaskBase& ) = delete; | ^ unifrac_task.hpp:156:37: note: remove the '< >' unifrac_task.hpp:328:32: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 328 | UnifracTask(const UnifracTask& ) = delete; | ^ unifrac_task.hpp:328:32: note: remove the '< >' unifrac_task.hpp:360:48: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 360 | UnifracUnnormalizedWeightedTask(const UnifracUnnormalizedWeightedTask& ) = delete; | ^ unifrac_task.hpp:360:48: note: remove the '< >' unifrac_task.hpp:398:46: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 398 | UnifracNormalizedWeightedTask(const UnifracNormalizedWeightedTask& ) = delete; | ^ unifrac_task.hpp:398:46: note: remove the '< >' unifrac_task.hpp:441:38: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 441 | UnifracUnweightedTask(const UnifracUnweightedTask& ) = delete; | ^ unifrac_task.hpp:441:38: note: remove the '< >' unifrac_task.hpp:473:39: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 473 | UnifracGeneralizedTask(const UnifracGeneralizedTask& ) = delete; | ^ unifrac_task.hpp:473:39: note: remove the '< >' unifrac_task.hpp:542:35: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 542 | UnifracVawTask(const UnifracVawTask& ) = delete; | ^ unifrac_task.hpp:542:35: note: remove the '< >' unifrac_task.hpp:582:51: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 582 | UnifracVawUnnormalizedWeightedTask(const UnifracVawUnnormalizedWeightedTask& ) = delete; | ^ unifrac_task.hpp:582:51: note: remove the '< >' unifrac_task.hpp:597:49: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 597 | UnifracVawNormalizedWeightedTask(const UnifracVawNormalizedWeightedTask& ) = delete; | ^ unifrac_task.hpp:597:49: note: remove the '< >' unifrac_task.hpp:612:41: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 612 | UnifracVawUnweightedTask(const UnifracVawUnweightedTask& ) = delete; | ^ unifrac_task.hpp:612:41: note: remove the '< >' unifrac_task.hpp:627:42: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 627 | UnifracVawGeneralizedTask(const UnifracVawGeneralizedTask& ) = delete; | ^ unifrac_task.hpp:627:42: note: remove the '< >' 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 226 | unifracTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 229 | unifracTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 232 | unifracTT,double>( table, tree, false, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 235 | unifracTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 238 | unifracTT,float>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 241 | unifracTT,float>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 244 | unifracTT,float>( table, tree, false, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 247 | unifracTT,float>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 383 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 386 | unifrac_vawTT,double>( table, tree, false, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 389 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 395 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 398 | unifrac_vawTT,float >( table, tree, false, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 401 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/build/reproducible-path/unifrac-tools-1.4/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/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu_cpu_basic.so; cp -a libssu_cpu_basic.so* /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ssu_cpu_basic; cp ssu_cpu_basic /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/faithpd_cpu_basic; cp faithpd_cpu_basic /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make clean && make api /bin/sh: line 1: ./setup_nv_h5.sh: No such file or directory make[2]: *** [Makefile:43: api_nv_avx2] Error 1 make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr returned exit code 2 make[1]: *** [debian/rules:15: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /srv/workspace/pbuilder/388004/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Tue Jan 7 18:19:29 UTC 2025 Filesystem Size Used Avail Use% Mounted on tmpfs 30G 0 30G 0% /dev/shm I: user script /srv/workspace/pbuilder/388004/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/388004 and its subdirectories