I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 28 02:51:23 -12 2025 I: pbuilder-time-stamp: 1738075883 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/20388/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='ecb223d298c94a2b87d14d08a541600a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='20388' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JRj784fe/pbuilderrc_z8Ch --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JRj784fe/b1 --logfile b1/build.log unifrac-tools_1.4-3.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/20388/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: armhf 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 ... 19568 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-arm-linux-gnueabihf{a} gfortran-arm-linux-gnueabihf{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-dev{a} libldap2{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 60.4 MB of archives. After unpacking 209 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.1-3 [844 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.1-3 [1840 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2025a-1 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-6 [146 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.1-3 [1850 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.1-3 [740 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.4-2 [84.6 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf automake all 1:1.17-2 [861 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf chrpath armhf 0.18-1 [12.6 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.2-1 [55.1 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.24.1 [90.9 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-2 [539 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 39 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf debhelper all 13.24.1 [920 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf dh-exec armhf 0.30 [24.3 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-15 [263 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libgfortran-14-dev armhf 14.2.0-15 [315 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-15 [8723 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf gfortran-14 armhf 14.2.0-15 [13.5 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1 [1288 B] Get: 54 http://deb.debian.org/debian unstable/main armhf gfortran armhf 4:14.2.0-1 [1428 B] Get: 55 http://deb.debian.org/debian unstable/main armhf hdf5-helpers armhf 1.14.5+repack-3 [26.6 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-4 [30.3 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-4 [75.8 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 59 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-4 [285 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-4 [116 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-4 [52.6 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-4 [37.5 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-4 [37.3 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-4 [47.4 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-4 [126 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libaec0 armhf 1.1.3-1+b1 [21.9 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libsz2 armhf 1.1.3-1+b1 [8036 B] Get: 68 http://deb.debian.org/debian unstable/main armhf libaec-dev armhf 1.1.3-1+b1 [19.3 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.1-2 [116 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libblas-dev armhf 3.12.1-2 [127 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8+b1 [18.6 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8+b1 [50.6 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libldap2 armhf 2.6.9+dfsg-1 [167 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libtasn1-6 armhf 4.19.0-3+b3 [43.9 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libgnutls30t64 armhf 3.8.8-2 [1370 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.11.1-1+b1 [304 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-4 [15.9 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libldap-dev armhf 2.6.9+dfsg-1 [286 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3 [328 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3 [592 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1+b1 [539 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-3 [208 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf libssl-dev armhf 3.4.0-2 [2431 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [326 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf libcurl4-openssl-dev armhf 8.11.1-1+b1 [425 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf libhdf5-310 armhf 1.14.5+repack-3 [1272 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf libhdf5-cpp-310 armhf 1.14.5+repack-3 [125 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf libhdf5-fortran-310 armhf 1.14.5+repack-3 [102 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [67.3 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-fortran-310 armhf 1.14.5+repack-3 [38.3 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-cpp-310 armhf 1.14.5+repack-3 [24.1 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-3+b1 [263 kB] Get: 117 http://deb.debian.org/debian unstable/main armhf libjpeg-dev armhf 1:2.1.5-3+b1 [72.2 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf libhdf5-dev armhf 1.14.5+repack-3 [3091 kB] Get: 119 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.1-2 [1835 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf liblapack-dev armhf 3.12.1-2 [1935 kB] Get: 121 http://deb.debian.org/debian unstable/main armhf libtmglib3 armhf 3.12.1-2 [90.4 kB] Get: 122 http://deb.debian.org/debian unstable/main armhf liblapacke armhf 3.12.1-2 [309 kB] Get: 123 http://deb.debian.org/debian unstable/main armhf libtmglib-dev armhf 3.12.1-2 [93.4 kB] Get: 124 http://deb.debian.org/debian unstable/main armhf liblapacke-dev armhf 3.12.1-2 [325 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf libxxhash-dev armhf 0.8.3-2 [91.2 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf liblz4-dev armhf 1.10.0-3 [77.5 kB] Fetched 60.4 MB in 5s (11.6 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:armhf. (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 ... 19568 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_armhf.deb ... Unpacking libpython3.13-minimal:armhf (3.13.1-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:armhf. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_armhf.deb ... Unpacking libpython3.13-stdlib:armhf (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_armhf.deb ... Unpacking python3.13 (3.13.1-3) ... 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Setting up libblas3:armhf (3.12.1-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libunbound8:armhf (1.22.0-1+b1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-3+b1) ... Setting up comerr-dev:armhf (2.1-1.47.2-1) ... Setting up libunistring5:armhf (1.3-1) ... Setting up libssl-dev:armhf (3.4.0-2) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-4) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:armhf (14.2.0-15) ... Setting up autoconf (2.72-3) ... Setting up libxxhash-dev:armhf (0.8.3-2) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:armhf (3.4.6-1) ... 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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 librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:armhf (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:armhf (1.21.3-4) ... Setting up libhdf5-fortran-310:armhf (1.14.5+repack-3) ... Setting up krb5-multidev:armhf (1.21.3-4) ... Setting up libhdf5-cpp-310:armhf (1.14.5+repack-3) ... Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... Setting up libkrb5-dev:armhf (1.21.3-4) ... Setting up libcurl4-openssl-dev:armhf (8.11.1-1+b1) ... Setting up libhdf5-hl-cpp-310:armhf (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:armhf (1.14.5+repack-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.40-6) ... 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: Running cd /build/reproducible-path/unifrac-tools-1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 armhf 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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); | ^~~~~~ 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 135 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 'TData* malloc_wcheck(unsigned int) [with TData = double]': biom_inmem.cpp:99:60: required from here 99 | obs_data_resident[i] = malloc_wcheck(cnt); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int]': biom_inmem.cpp:100:62: required from here 100 | obs_indices_resident[i] = malloc_wcheck(cnt); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int*]': biom_inmem.cpp:177:55: required from here 177 | obs_indices_resident = malloc_wcheck(n_obs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double*]': biom_inmem.cpp:178:55: required from here 178 | obs_data_resident = malloc_wcheck(n_obs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} 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 '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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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: 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 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 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: '__off64_t' {aka 'long long int'} and 'uint64_t' {aka 'long 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: '__off64_t' {aka 'long long int'} and 'uint64_t' {aka 'long 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 '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, __off64_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, __off64_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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': unifrac_cmp.cpp:281:29: required from '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]' 281 | initialize_sample_counts(sample_total_counts, task_p, table); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = float]': unifrac_cmp.cpp:281:29: required from '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]' 281 | initialize_sample_counts(sample_total_counts, task_p, table); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = double; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:380:77: required from here 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = float; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:392:77: required from here 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' 320 | : UnifracTaskBase(_dm_stripes, _dm_stripes_total, _max_embs, _task_p) {} | ^ unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' 428 | : UnifracTask(_dm_stripes,_dm_stripes_total,_max_embs,_task_p) | ^ unifrac_cmp.cpp:89:11: required from '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]' 89 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total),max_emb,task_p); | ^~~~~~~ unifrac_cmp.cpp:226:70: required from here 226 | unifracTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' 320 | : UnifracTaskBase(_dm_stripes, _dm_stripes_total, _max_embs, _task_p) {} | ^ unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' 428 | : UnifracTask(_dm_stripes,_dm_stripes_total,_max_embs,_task_p) | ^ unifrac_cmp.cpp:89:11: required from '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]' 89 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total),max_emb,task_p); | ^~~~~~~ unifrac_cmp.cpp:238:69: required from here 238 | unifracTT,float>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ^ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:380:77: required from here 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ^ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:392:77: required from here 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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: 1: source: not found make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f *.o ssu_nv_avx2 faithpd_nv_avx2 test_su test_ska test_api libssu_nv_avx2.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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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); | ^~~~~~ 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 135 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 'TData* malloc_wcheck(unsigned int) [with TData = double]': biom_inmem.cpp:99:60: required from here 99 | obs_data_resident[i] = malloc_wcheck(cnt); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int]': biom_inmem.cpp:100:62: required from here 100 | obs_indices_resident[i] = malloc_wcheck(cnt); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int*]': biom_inmem.cpp:177:55: required from here 177 | obs_indices_resident = malloc_wcheck(n_obs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double*]': biom_inmem.cpp:178:55: required from here 178 | obs_data_resident = malloc_wcheck(n_obs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} 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 '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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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: 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 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 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: '__off64_t' {aka 'long long int'} and 'uint64_t' {aka 'long 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: '__off64_t' {aka 'long long int'} and 'uint64_t' {aka 'long 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 '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, __off64_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, __off64_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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': unifrac_cmp.cpp:281:29: required from '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]' 281 | initialize_sample_counts(sample_total_counts, task_p, table); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = float]': unifrac_cmp.cpp:281:29: required from '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]' 281 | initialize_sample_counts(sample_total_counts, task_p, table); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = double; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:380:77: required from here 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = float; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:392:77: required from here 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' 320 | : UnifracTaskBase(_dm_stripes, _dm_stripes_total, _max_embs, _task_p) {} | ^ unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' 428 | : UnifracTask(_dm_stripes,_dm_stripes_total,_max_embs,_task_p) | ^ unifrac_cmp.cpp:89:11: required from '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]' 89 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total),max_emb,task_p); | ^~~~~~~ unifrac_cmp.cpp:226:70: required from here 226 | unifracTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' 320 | : UnifracTaskBase(_dm_stripes, _dm_stripes_total, _max_embs, _task_p) {} | ^ unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' 428 | : UnifracTask(_dm_stripes,_dm_stripes_total,_max_embs,_task_p) | ^ unifrac_cmp.cpp:89:11: required from '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]' 89 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total),max_emb,task_p); | ^~~~~~~ unifrac_cmp.cpp:238:69: required from here 238 | unifracTT,float>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ^ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:380:77: required from here 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ^ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:392:77: required from here 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int 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/build/reproducible-path/unifrac-tools-1.4/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/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib 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 main /bin/sh: 1: source: not found 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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_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 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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_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 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' 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 '/build/reproducible-path/unifrac-tools-1.4/src' rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu_nv_avx2.so; cp -a libssu_nv_avx2.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_nv_avx2; cp ssu_nv_avx2 /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_nv_avx2; cp faithpd_nv_avx2 /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 ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make clean && make api /bin/sh: 1: source: not found make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f *.o ssu_nv faithpd_nv test_su test_ska test_api libssu_nv.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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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); | ^~~~~~ 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 135 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 'TData* malloc_wcheck(unsigned int) [with TData = double]': biom_inmem.cpp:99:60: required from here 99 | obs_data_resident[i] = malloc_wcheck(cnt); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int]': biom_inmem.cpp:100:62: required from here 100 | obs_indices_resident[i] = malloc_wcheck(cnt); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int*]': biom_inmem.cpp:177:55: required from here 177 | obs_indices_resident = malloc_wcheck(n_obs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double*]': biom_inmem.cpp:178:55: required from here 178 | obs_data_resident = malloc_wcheck(n_obs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} 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 '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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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: 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 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 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: '__off64_t' {aka 'long long int'} and 'uint64_t' {aka 'long 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: '__off64_t' {aka 'long long int'} and 'uint64_t' {aka 'long 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 '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, __off64_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, __off64_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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': unifrac_cmp.cpp:281:29: required from '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]' 281 | initialize_sample_counts(sample_total_counts, task_p, table); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = float]': unifrac_cmp.cpp:281:29: required from '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]' 281 | initialize_sample_counts(sample_total_counts, task_p, table); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = double; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:380:77: required from here 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = float; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:392:77: required from here 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' 320 | : UnifracTaskBase(_dm_stripes, _dm_stripes_total, _max_embs, _task_p) {} | ^ unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' 428 | : UnifracTask(_dm_stripes,_dm_stripes_total,_max_embs,_task_p) | ^ unifrac_cmp.cpp:89:11: required from '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]' 89 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total),max_emb,task_p); | ^~~~~~~ unifrac_cmp.cpp:226:70: required from here 226 | unifracTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' 320 | : UnifracTaskBase(_dm_stripes, _dm_stripes_total, _max_embs, _task_p) {} | ^ unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' 428 | : UnifracTask(_dm_stripes,_dm_stripes_total,_max_embs,_task_p) | ^ unifrac_cmp.cpp:89:11: required from '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]' 89 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total),max_emb,task_p); | ^~~~~~~ unifrac_cmp.cpp:238:69: required from here 238 | unifracTT,float>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ^ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:380:77: required from here 380 | unifrac_vawTT,double>( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 144 | , embedded_proportions(initialize_embedded(dm_stripes.n_samples_r,_max_embs)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' 532 | , embedded_counts(UnifracTaskBase::initialize_embedded(this->dm_stripes.n_samples_r,_max_embs)), sample_total_counts(_sample_total_counts) {} | ^ unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' 610 | : UnifracVawTask(_dm_stripes,_dm_stripes_total,_sample_total_counts,_max_embs,_task_p) {} | ^ unifrac_cmp.cpp:285:11: required from '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]' 285 | TaskT taskObj(std::ref(dm_stripes), std::ref(dm_stripes_total), sample_total_counts, max_emb, task_p); | ^~~~~~~ unifrac_cmp.cpp:392:77: required from here 392 | unifrac_vawTT,float >( table, tree, true, dm_stripes,dm_stripes_total,task_p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int 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/build/reproducible-path/unifrac-tools-1.4/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/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/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 '/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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_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 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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_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 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' 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 '/build/reproducible-path/unifrac-tools-1.4/src' rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu_nv.so; cp -a libssu_nv.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_nv; cp ssu_nv /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_nv; cp faithpd_nv /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' cd combined && make api make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/combined' cc -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -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 -c libssu.c -fPIC cc -shared -o libssu.so libssu.o -fPIC -ldl -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/combined' cd combined && make install make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/combined' rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu.so; cp libssu.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; cp ssu /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; cp faithpd /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/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 '/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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 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' # use the default compiler for the test subdir as it tests the combined shlib cd test && make test_binaries make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/test' cc -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 -std=c99 -O0 -g capi_test.c -I../src -lssu -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -Wl,-rpath,/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -Wl,-z,relro -Wl,-z,now -o capi_test make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/test' make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' chmod +x /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/* make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' export PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin ; \ cd ci ; \ ./crawford_test.sh All tests succeeded make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel debian/rules override_dh_auto_install 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_install -- PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr make -j1 install DESTDIR=/build/reproducible-path/unifrac-tools-1.4/debian/tmp AM_UPDATE_INFO_DIR=no "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' cd src && make install make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' h5c++ -shared -fopenmp -shlib -o libssu.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.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.so.0 libssu.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 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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++ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu.so; cp -a libssu.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; cp ssu /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; cp faithpd /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' make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' chrpath -d debian/tmp/usr/bin/ssu chrpath -d debian/tmp/usr/bin/faithpd chrpath -d debian/tmp/usr/lib/libssu.so* dh_install make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libssu0/usr/lib/arm-linux-gnueabihf/libssu.so.0 found in none of the libraries dpkg-shlibdeps: warning: debian/unifrac-tools/usr/bin/faithpd contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/unifrac-tools/usr/bin/ssu contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dpkg-gencontrol: warning: Depends field of package libssu-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'unifrac-tools' in '../unifrac-tools_1.4-3_armhf.deb'. dpkg-deb: building package 'libssu0' in '../libssu0_1.4-3_armhf.deb'. dpkg-deb: building package 'libssu-dev' in '../libssu-dev_1.4-3_armhf.deb'. dpkg-deb: building package 'libssu0-dbgsym' in '../libssu0-dbgsym_1.4-3_armhf.deb'. dpkg-deb: building package 'unifrac-tools-dbgsym' in '../unifrac-tools-dbgsym_1.4-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../unifrac-tools_1.4-3_armhf.buildinfo dpkg-genchanges --build=binary -O../unifrac-tools_1.4-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/20388 and its subdirectories I: Current time: Tue Jan 28 02:57:41 -12 2025 I: pbuilder-time-stamp: 1738076261