Fri Feb 14 05:35:45 UTC 2025 I: starting to build sga/trixie/arm64 on jenkins on '2025-02-14 05:35' Fri Feb 14 05:35:45 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/79447/console.log Fri Feb 14 05:35:45 UTC 2025 I: Downloading source for trixie/sga=0.10.15-7 --2025-02-14 05:35:45-- http://deb.debian.org/debian/pool/main/s/sga/sga_0.10.15-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2084 (2.0K) [text/prs.lines.tag] Saving to: ‘sga_0.10.15-7.dsc’ 0K .. 100% 358M=0s 2025-02-14 05:35:45 (358 MB/s) - ‘sga_0.10.15-7.dsc’ saved [2084/2084] Fri Feb 14 05:35:45 UTC 2025 I: sga_0.10.15-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sga Binary: sga Architecture: any Version: 0.10.15-7 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://github.com/jts/sga Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/sga Vcs-Git: https://salsa.debian.org/med-team/sga.git Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools , python3 , python3-ruffus , python3-pysam Package-List: sga deb science optional arch=any Checksums-Sha1: 55b540d2f1cae3a44de8da6db8f413826bdb5f14 6569986 sga_0.10.15.orig.tar.gz 4598b0bf58446b932f202a8bfa7e9d9d3bc018de 214356 sga_0.10.15-7.debian.tar.xz Checksums-Sha256: 1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b 6569986 sga_0.10.15.orig.tar.gz 708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f 214356 sga_0.10.15-7.debian.tar.xz Files: 990aed1593f8072650c6366e5cf32519 6569986 sga_0.10.15.orig.tar.gz 420c1f46b48f89950ac7e500402215e8 214356 sga_0.10.15-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmFEoJwACgkQPCZ2P2xn 5uIThw/5AcAmhXJYwdZ93J6fhmzcEOSTkqi8GdH/9Nlt3BCVIZlJR3/6vcttoVUo sKob/Rr78LGESV215LOC13J9soUrZa6giB6aM+wU+hVhD81dCt7zz2bsMSvwopC8 DNmWt3cZta4xDM7MxuBL5cztJZThE8ewwbZ3VQmGHix/aAMOlcK2EsP9iQCpRepF Ovmc4kDe1USc6erpE3cohGVlHfoJy4JXggHjvKqHz4u4YGFLQNpHpT70LH9HSrgh thqrPnnI9I2CjNxF2WSYIFMCD5f1Iq9TWihNi4H6m0keRgZcFE1lKjKuP8WYT9rK GLvaAGaLC1sB0BZ0lLpf18pySxNUzA/EtX6RzBes0UMRG9SkWG2lOFTyZRJjhC/3 Mz3FGKLROVKjTOerTgdhDKCoAPa/VLwXIYZLX/xxHxVelJibqPHRlWuS6xaJkunW OzPueUfUSynrS9kQZ5bM0CIfmhl+9zqWKNIfvwRDqmTh5meaH/oYneMgUIKSJgLa PBU8/Qc+FzpObFe71EIRa/5vs+kUQcvLIoeFqYMoDLd5WFwyFlTTe035u4SKpA7q EOADJZbbLzqBP89tgkWjglsUCVClDBUeyuocQXREI85kW9GkoWnwvKqkZaRNncxO UdqDEwW4NwADMhzii6hdLiJxBiYBhcLkP+ciz4TxX2wUKU6qO1U= =KU9x -----END PGP SIGNATURE----- Fri Feb 14 05:35:45 UTC 2025 I: Checking whether the package is not for us Fri Feb 14 05:35:45 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Fri Feb 14 05:35:45 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Fri Feb 14 05:39:16 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Mar 18 23:58:47 -12 2026 I: pbuilder-time-stamp: 1773921527 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [sga_0.10.15-7.dsc] I: copying [./sga_0.10.15.orig.tar.gz] I: copying [./sga_0.10.15-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./sga_0.10.15-7.dsc: unsupported subcommand dpkg-source: info: extracting sga in sga-0.10.15 dpkg-source: info: unpacking sga_0.10.15.orig.tar.gz dpkg-source: info: unpacking sga_0.10.15-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002-no-rpath.patch dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch dpkg-source: info: applying 0006-remove-google-addsense.patch dpkg-source: info: applying gcc-7.patch dpkg-source: info: applying no_privacy_breach_url.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying no_enforcing_c++98.patch dpkg-source: info: applying gcc9.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3066102/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='61054384ae3c44ceb1726cdd0a5ac06a' 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='3066102' 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.TlCvmfAt/pbuilderrc_EKg5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TlCvmfAt/b1 --logfile b1/build.log sga_0.10.15-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3066102/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools, python3, python3-ruffus, python3-pysam dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19922 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev | libz-dev; however: Package zlib1g-dev is not installed. Package libz-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-ruffus; however: Package python3-ruffus is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} help2man{a} intltool-debian{a} libabsl20230802{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbamtools-dev{a} libbamtools2.5.2{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcom-err2{a} libcurl3t64-gnutls{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} libldap2{a} liblerc4{a} liblocale-gettext-perl{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libsparsehash-dev{a} libssh2-1t64{a} libsvtav1enc2{a} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-pysam{a} python3-ruffus{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-liberation krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 157 newly installed, 0 to remove and 0 not upgraded. Need to get 57.0 MB of archives. After unpacking 240 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 52 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.46-4 [276 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-2 [462 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libcdt5 arm64 2.42.4-2+b4 [39.4 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libcgraph6 arm64 2.42.4-2+b4 [61.4 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libaom3 arm64 3.12.0-1 [1672 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgav1-1 arm64 0.19.0-3 [491 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 librav1e0.7 arm64 0.7.1-9+b1 [661 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libyuv0 arm64 0.0.1904.20250204-1 [137 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-dav1d arm64 1.19.5-1+b1 [11.5 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-libde265 arm64 1.19.5-1+b1 [15.4 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libheif1 arm64 1.19.5-1+b1 [438 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.83.3-2 [1421 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.5.4-3 [415 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libpathplan4 arm64 2.42.4-2+b4 [41.4 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libgvc6 arm64 2.42.4-2+b4 [628 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libgvpr2 arm64 2.42.4-2+b4 [182 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblab-gamut1 arm64 2.42.4-2+b4 [198 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 graphviz arm64 2.42.4-2+b4 [571 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-6+b1 [141 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libbamtools-dev arm64 2.5.2+dfsg-6+b1 [210 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 138 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.12.0+git20250209.89ed161+ds-1 [336 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.21+ds-1 [426 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5+20250125-2 [96.2 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.23.0+ds-1 [4160 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-ruffus all 2.8.4-7 [151 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.21-1 [637 kB] Fetched 57.0 MB in 1s (57.0 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19922 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... 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Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... 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Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 19 11:59:33 UTC 2026. Universal Time is now: Thu Mar 19 11:59:33 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up libpathplan4:arm64 (2.42.4-2+b4) ... Setting up libann0 (1.1.2+doc-9+b2) ... Setting up libncurses6:arm64 (6.5+20250125-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.46-4) ... Setting up autopoint (0.23.1-1) ... 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Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up libglib2.0-0t64:arm64 (2.83.3-2) ... No schema files found: doing nothing. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libbamtools-dev:arm64 (2.5.2+dfsg-6+b1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up libgav1-1:arm64 (0.19.0-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgvpr2:arm64 (2.42.4-2+b4) ... Setting up groff-base (1.23.0-7) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-2) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libavif16:arm64 (1.1.1-1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.56.1-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ... 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Setting up python3-ruffus (2.8.4-7) ... /usr/lib/python3/dist-packages/ruffus/test/draw_specified_dependency_tree.py:112: SyntaxWarning: invalid escape sequence '\[' attributes = re.compile("\[.+\]") 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/sga-0.10.15/ && 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 > ../sga_0.10.15-7_source.changes dpkg-buildpackage: info: source package sga dpkg-buildpackage: info: source version 0.10.15-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --with python3 --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src configure.ac:7: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:24: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/m4_ax_openmp.m4:70: AX_OPENMP is expanded from... configure.ac:24: the top level configure.ac:12: installing './compile' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Algorithm/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/sga-0.10.15' dh_auto_configure -- --with-bamtools=/usr/ cd src && ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-bamtools=/usr/ checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing clock_gettime... none required checking for OpenMP flag of C++ compiler... -fopenmp checking for host type... you are not using osx so multi-threading should work. checking for google/sparse_hash_set... yes checking for google/sparse_hash_set... (cached) yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for ext/hash_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for ext/hash_set... yes checking for api/BamReader.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating Thirdparty/Makefile config.status: creating Util/Makefile config.status: creating SQG/Makefile config.status: creating Bigraph/Makefile config.status: creating Algorithm/Makefile config.status: creating StringGraph/Makefile config.status: creating Concurrency/Makefile config.status: creating SuffixTools/Makefile config.status: creating GraphDiff/Makefile config.status: creating Scaffold/Makefile config.status: creating SGA/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/sga-0.10.15' dh_auto_build -O--sourcedirectory=src cd src && make -j12 make[1]: Entering directory '/build/reproducible-path/sga-0.10.15/src' make all-recursive make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src' Making all in bin make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/bin' cp -n sga-bam2de.pl sga-bam2de cp -n sga-mergeDriver.pl sga-mergeDriver make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/bin' Making all in Thirdparty make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o gzstream.o gzstream.C gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o stdaln.o stdaln.c g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o overlapper.o overlapper.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o multiple_alignment.o multiple_alignment.cpp gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o bcr.o bcr.c g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o MurmurHash3.o MurmurHash3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o count_min_sketch.o count_min_sketch.cpp MurmurHash3.cpp: In function 'void MurmurHash3_x86_32(const void*, int, uint32_t, void*)': MurmurHash3.cpp:132:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 132 | case 3: k1 ^= tail[2] << 16; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:133:3: note: here 133 | case 2: k1 ^= tail[1] << 8; | ^~~~ MurmurHash3.cpp:133:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 133 | case 2: k1 ^= tail[1] << 8; | ~~~^~~~~~~~~~~~~~~ MurmurHash3.cpp:134:3: note: here 134 | case 1: k1 ^= tail[0]; | ^~~~ MurmurHash3.cpp: In function 'void MurmurHash3_x86_128(const void*, int, uint32_t, void*)': MurmurHash3.cpp:207:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 207 | case 15: k4 ^= tail[14] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:208:3: note: here 208 | case 14: k4 ^= tail[13] << 8; | ^~~~ MurmurHash3.cpp:208:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 208 | case 14: k4 ^= tail[13] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:209:3: note: here 209 | case 13: k4 ^= tail[12] << 0; | ^~~~ MurmurHash3.cpp:210:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 210 | k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4; | ~~~^~~~~ MurmurHash3.cpp:212:3: note: here 212 | case 12: k3 ^= tail[11] << 24; | ^~~~ MurmurHash3.cpp:212:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 212 | case 12: k3 ^= tail[11] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:213:3: note: here 213 | case 11: k3 ^= tail[10] << 16; | ^~~~ MurmurHash3.cpp:213:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 213 | case 11: k3 ^= tail[10] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:214:3: note: here 214 | case 10: k3 ^= tail[ 9] << 8; | ^~~~ MurmurHash3.cpp:214:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 214 | case 10: k3 ^= tail[ 9] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:215:3: note: here 215 | case 9: k3 ^= tail[ 8] << 0; | ^~~~ MurmurHash3.cpp:216:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 216 | k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3; | ~~~^~~~~ MurmurHash3.cpp:218:3: note: here 218 | case 8: k2 ^= tail[ 7] << 24; | ^~~~ MurmurHash3.cpp:218:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 218 | case 8: k2 ^= tail[ 7] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:219:3: note: here 219 | case 7: k2 ^= tail[ 6] << 16; | ^~~~ MurmurHash3.cpp:219:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 219 | case 7: k2 ^= tail[ 6] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:220:3: note: here 220 | case 6: k2 ^= tail[ 5] << 8; | ^~~~ MurmurHash3.cpp:220:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 220 | case 6: k2 ^= tail[ 5] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:221:3: note: here 221 | case 5: k2 ^= tail[ 4] << 0; | ^~~~ MurmurHash3.cpp:222:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 222 | k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2; | ~~~^~~~~ MurmurHash3.cpp:224:3: note: here 224 | case 4: k1 ^= tail[ 3] << 24; | ^~~~ MurmurHash3.cpp:224:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 224 | case 4: k1 ^= tail[ 3] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:225:3: note: here 225 | case 3: k1 ^= tail[ 2] << 16; | ^~~~ MurmurHash3.cpp:225:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 225 | case 3: k1 ^= tail[ 2] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:226:3: note: here 226 | case 2: k1 ^= tail[ 1] << 8; | ^~~~ MurmurHash3.cpp:226:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 226 | case 2: k1 ^= tail[ 1] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:227:3: note: here 227 | case 1: k1 ^= tail[ 0] << 0; | ^~~~ MurmurHash3.cpp: In function 'void MurmurHash3_x64_128(const void*, int, uint32_t, void*)': MurmurHash3.cpp:296:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 296 | case 15: k2 ^= uint64_t(tail[14]) << 48; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:297:3: note: here 297 | case 14: k2 ^= uint64_t(tail[13]) << 40; | ^~~~ MurmurHash3.cpp:297:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 297 | case 14: k2 ^= uint64_t(tail[13]) << 40; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:298:3: note: here 298 | case 13: k2 ^= uint64_t(tail[12]) << 32; | ^~~~ MurmurHash3.cpp:298:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 298 | case 13: k2 ^= uint64_t(tail[12]) << 32; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:299:3: note: here 299 | case 12: k2 ^= uint64_t(tail[11]) << 24; | ^~~~ MurmurHash3.cpp:299:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 299 | case 12: k2 ^= uint64_t(tail[11]) << 24; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:300:3: note: here 300 | case 11: k2 ^= uint64_t(tail[10]) << 16; | ^~~~ MurmurHash3.cpp:300:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 300 | case 11: k2 ^= uint64_t(tail[10]) << 16; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:301:3: note: here 301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8; | ^~~~ MurmurHash3.cpp:301:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:302:3: note: here 302 | case 9: k2 ^= uint64_t(tail[ 8]) << 0; | ^~~~ MurmurHash3.cpp:303:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 303 | k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2; | ~~~^~~~~ MurmurHash3.cpp:305:3: note: here 305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56; | ^~~~ MurmurHash3.cpp:305:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:306:3: note: here 306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48; | ^~~~ MurmurHash3.cpp:306:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:307:3: note: here 307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40; | ^~~~ MurmurHash3.cpp:307:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:308:3: note: here 308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32; | ^~~~ MurmurHash3.cpp:308:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:309:3: note: here 309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24; | ^~~~ MurmurHash3.cpp:309:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:310:3: note: here 310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16; | ^~~~ MurmurHash3.cpp:310:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:311:3: note: here 311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8; | ^~~~ MurmurHash3.cpp:311:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:312:3: note: here 312 | case 1: k1 ^= uint64_t(tail[ 0]) << 0; | ^~~~ bcr.c: In function 'ld_restore': bcr.c:183:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | fread(&ld->max, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:186:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 186 | fread(&x, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:189:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fread(ld->a[i], 8, x, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s1_start' [-Wmissing-field-initializers] 37 | OverlapperParams default_params = { 2, -6, -3, -2, ALT_OVERLAP }; | ^ overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s1_end' [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s2_start' [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s2_end' [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::use_m_ops' [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s1_start' [-Wmissing-field-initializers] 38 | OverlapperParams ungapped_params = { 2, -10000, -3, -2, ALT_OVERLAP }; | ^ overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s1_end' [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s2_start' [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s2_end' [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::use_m_ops' [-Wmissing-field-initializers] stdaln.c: In function 'aln_local_core': stdaln.c:756:17: warning: 'free' called on pointer '*(int **)((char *))' with nonzero offset 4 [-Wfree-nonheap-object] 756 | free(s_array[i]); | ^~~~~~~~~~~~~~~~ rm -f libthirdparty.a ar cr libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ranlib libthirdparty.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' Making all in Util make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Util' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Util.o `test -f 'Util.cpp' || echo './'`Util.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Alphabet.o `test -f 'Alphabet.cpp' || echo './'`Alphabet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Contig.o `test -f 'Contig.cpp' || echo './'`Contig.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-ReadInfoTable.o `test -f 'ReadInfoTable.cpp' || echo './'`ReadInfoTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-SeqReader.o `test -f 'SeqReader.cpp' || echo './'`SeqReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-DNAString.o `test -f 'DNAString.cpp' || echo './'`DNAString.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Match.o `test -f 'Match.cpp' || echo './'`Match.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Pileup.o `test -f 'Pileup.cpp' || echo './'`Pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-BitChar.o `test -f 'BitChar.cpp' || echo './'`BitChar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Interval.o `test -f 'Interval.cpp' || echo './'`Interval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-SeqCoord.o `test -f 'SeqCoord.cpp' || echo './'`SeqCoord.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-MultiOverlap.o `test -f 'MultiOverlap.cpp' || echo './'`MultiOverlap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-QualityVector.o `test -f 'QualityVector.cpp' || echo './'`QualityVector.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.cpp In file included from Pileup.h:12, from Pileup.cpp:10: Pileup.cpp: In member function 'DNADouble Pileup::calculateSimpleAlphaProb() const': Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ Pileup.cpp:46:5: note: in expansion of macro 'WARN_ONCE' 46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability"); | ^~~~~~~~~ Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ Pileup.cpp:46:5: note: in expansion of macro 'WARN_ONCE' 46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability"); | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-PrimerScreen.o `test -f 'PrimerScreen.cpp' || echo './'`PrimerScreen.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-CorrectionThresholds.o `test -f 'CorrectionThresholds.cpp' || echo './'`CorrectionThresholds.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-StdAlnTools.o `test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-QualityTable.o `test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp rm -f libutil.a ar cr libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o ranlib libutil.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Util' Making all in SQG make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SQG' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsqg_a-SQG.o `test -f 'SQG.cpp' || echo './'`SQG.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp rm -f libsqg.a ar cr libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ranlib libsqg.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SQG' Making all in Bigraph make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libbigraph_a-Bigraph.o `test -f 'Bigraph.cpp' || echo './'`Bigraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libbigraph_a-Vertex.o `test -f 'Vertex.cpp' || echo './'`Vertex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libbigraph_a-Edge.o `test -f 'Edge.cpp' || echo './'`Edge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp In file included from ../Util/EncodedString.h:22, from Vertex.h:23, from Vertex.cpp:9: ../Util/EncodedString.h: In instantiation of 'void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]': ../Util/EncodedString.h:43:18: required from 'EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]' 43 | _copy(other); | ~~~~~^~~~~~~ /usr/include/c++/14/bits/move.h:234:11: required from 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = EncodedString; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]' 234 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ Vertex.cpp:46:18: required from here 46 | std::swap(m_seq, label); | ~~~~~~~~~^~~~~~~~~~~~~~ ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ rm -f libbigraph.a ar cr libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ranlib libbigraph.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' Making all in Algorithm make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-OverlapAlgorithm.o `test -f 'OverlapAlgorithm.cpp' || echo './'`OverlapAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-SearchSeed.o `test -f 'SearchSeed.cpp' || echo './'`SearchSeed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-OverlapBlock.o `test -f 'OverlapBlock.cpp' || echo './'`OverlapBlock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-SearchHistory.o `test -f 'SearchHistory.cpp' || echo './'`SearchHistory.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-ErrorCorrectProcess.o `test -f 'ErrorCorrectProcess.cpp' || echo './'`ErrorCorrectProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-OverlapTools.o `test -f 'OverlapTools.cpp' || echo './'`OverlapTools.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-StringGraphGenerator.o `test -f 'StringGraphGenerator.cpp' || echo './'`StringGraphGenerator.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-FMMergeProcess.o `test -f 'FMMergeProcess.cpp' || echo './'`FMMergeProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-StatsProcess.o `test -f 'StatsProcess.cpp' || echo './'`StatsProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.cpp In file included from SearchHistory.h:12, from OverlapBlock.h:15, from OverlapBlock.cpp:11: OverlapBlock.cpp: In member function 'std::string OverlapBlock::getFullString(const std::string&) const': ../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ OverlapBlock.cpp:88:9: note: in expansion of macro 'WARN_ONCE' 88 | WARN_ONCE("getFullString() called on block with no history") | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ OverlapBlock.cpp:88:9: note: in expansion of macro 'WARN_ONCE' 88 | WARN_ONCE("getFullString() called on block with no history") | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-ReadCluster.o `test -f 'ReadCluster.cpp' || echo './'`ReadCluster.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-HaplotypeBuilder.o `test -f 'HaplotypeBuilder.cpp' || echo './'`HaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp rm -f libalgorithm.a ar cr libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o ranlib libalgorithm.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' Making all in StringGraph make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-SGUtil.o `test -f 'SGUtil.cpp' || echo './'`SGUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-SGAlgorithms.o `test -f 'SGAlgorithms.cpp' || echo './'`SGAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-SGVisitors.o `test -f 'SGVisitors.cpp' || echo './'`SGVisitors.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-CompleteOverlapSet.o `test -f 'CompleteOverlapSet.cpp' || echo './'`CompleteOverlapSet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-RemovalAlgorithm.o `test -f 'RemovalAlgorithm.cpp' || echo './'`RemovalAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-SGSearch.o `test -f 'SGSearch.cpp' || echo './'`SGSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libstringgraph_a-SGWalk.o `test -f 'SGWalk.cpp' || echo './'`SGWalk.cpp In file included from ../Bigraph/GraphCommon.h:14, from ../Bigraph/Bigraph.h:16, from SGAlgorithms.h:13, from SGAlgorithms.cpp:9: SGAlgorithms.cpp: In function 'Edge* SGAlgorithms::createEdgesFromOverlap(StringGraph*, const Overlap&, bool, size_t)': ../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ SGAlgorithms.cpp:60:9: note: in expansion of macro 'WARN_ONCE' 60 | WARN_ONCE("Edge limit reached for vertex when loading graph"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ SGAlgorithms.cpp:60:9: note: in expansion of macro 'WARN_ONCE' 60 | WARN_ONCE("Edge limit reached for vertex when loading graph"); | ^~~~~~~~~ rm -f libstringgraph.a ar cr libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o ranlib libstringgraph.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' Making all in Concurrency make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libconcurrency_a-OverlapProcess.o `test -f 'OverlapProcess.cpp' || echo './'`OverlapProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp rm -f libconcurrency.a ar cr libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ranlib libconcurrency.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' Making all in SuffixTools make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-STCommon.o `test -f 'STCommon.cpp' || echo './'`STCommon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-Occurrence.o `test -f 'Occurrence.cpp' || echo './'`Occurrence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SuffixArray.o `test -f 'SuffixArray.cpp' || echo './'`SuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SuffixCompare.o `test -f 'SuffixCompare.cpp' || echo './'`SuffixCompare.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-InverseSuffixArray.o `test -f 'InverseSuffixArray.cpp' || echo './'`InverseSuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SACAInducedCopying.o `test -f 'SACAInducedCopying.cpp' || echo './'`SACAInducedCopying.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTWriter.o `test -f 'BWTWriter.cpp' || echo './'`BWTWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SAReader.o `test -f 'SAReader.cpp' || echo './'`SAReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SAWriter.o `test -f 'SAWriter.cpp' || echo './'`SAWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp In file included from STCommon.cpp:9: In member function 'void SAElem::setID(uint64_t)', inlined from 'SAElem::SAElem(uint64_t)' at STCommon.cpp:19:10: STCommon.h:53:13: warning: '*this.SAElem::m_val' is used uninitialized [-Wuninitialized] 53 | m_val &= LOW_MASK; | ^~~~~ In member function 'void SAElem::setID(uint64_t)', inlined from 'SAElem::SAElem(uint64_t, uint64_t)' at STCommon.cpp:25:10: STCommon.h:53:13: warning: '*this.SAElem::m_val' is used uninitialized [-Wuninitialized] 53 | m_val &= LOW_MASK; | ^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-RankProcess.o `test -f 'RankProcess.cpp' || echo './'`RankProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.cpp In file included from ../Util/EncodedString.h:22, from Occurrence.h:13, from RLBWT.h:13, from BWT.h:18, from BWTDiskConstruction.h:19, from BWTDiskConstruction.cpp:12: ../Util/EncodedString.h: In instantiation of 'void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]': ../Util/EncodedString.h:43:18: required from 'EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]' 43 | _copy(other); | ~~~~~^~~~~~~ /usr/include/c++/14/bits/new_allocator.h:191:4: required from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]' 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:575:17: required from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]' 575 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc:117:30: required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >; reference = EncodedString&]' 117 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1301:21: required from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; value_type = EncodedString]' 1301 | { emplace_back(std::move(__x)); } | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ BWTDiskConstruction.cpp:252:36: required from here 252 | readSequences.push_back(item.seq.toString()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTWriterAscii.o `test -f 'BWTWriterAscii.cpp' || echo './'`BWTWriterAscii.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTReaderAscii.o `test -f 'BWTReaderAscii.cpp' || echo './'`BWTReaderAscii.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTIntervalCache.o `test -f 'BWTIntervalCache.cpp' || echo './'`BWTIntervalCache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-QuickBWT.o `test -f 'QuickBWT.cpp' || echo './'`QuickBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-SampledSuffixArray.o `test -f 'SampledSuffixArray.cpp' || echo './'`SampledSuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTCABauerCoxRosone.o `test -f 'BWTCABauerCoxRosone.cpp' || echo './'`BWTCABauerCoxRosone.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-BWTCARopebwt.o `test -f 'BWTCARopebwt.cpp' || echo './'`BWTCARopebwt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp rm -f libsuffixtools.a ar cr libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o ranlib libsuffixtools.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' Making all in Scaffold make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldVertex.o `test -f 'ScaffoldVertex.cpp' || echo './'`ScaffoldVertex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldEdge.o `test -f 'ScaffoldEdge.cpp' || echo './'`ScaffoldEdge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldGraph.o `test -f 'ScaffoldGraph.cpp' || echo './'`ScaffoldGraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldVisitors.o `test -f 'ScaffoldVisitors.cpp' || echo './'`ScaffoldVisitors.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldLink.o `test -f 'ScaffoldLink.cpp' || echo './'`ScaffoldLink.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldRecord.o `test -f 'ScaffoldRecord.cpp' || echo './'`ScaffoldRecord.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldGroup.o `test -f 'ScaffoldGroup.cpp' || echo './'`ScaffoldGroup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldAlgorithms.o `test -f 'ScaffoldAlgorithms.cpp' || echo './'`ScaffoldAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libscaffold_a-ScaffoldSequenceCollection.o `test -f 'ScaffoldSequenceCollection.cpp' || echo './'`ScaffoldSequenceCollection.cpp In file included from ../Bigraph/GraphCommon.h:14, from ../Bigraph/Bigraph.h:16, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: ScaffoldGroup.cpp: In member function 'void ScaffoldGroup::getSecondaryLinks()': ../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ ScaffoldGroup.cpp:279:13: note: in expansion of macro 'WARN_ONCE' 279 | WARN_ONCE("Recalculate xzDir"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ ScaffoldGroup.cpp:279:13: note: in expansion of macro 'WARN_ONCE' 279 | WARN_ONCE("Recalculate xzDir"); | ^~~~~~~~~ rm -f libscaffold.a ar cr libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o ranlib libscaffold.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' Making all in GraphDiff make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-DindelUtil.o `test -f 'DindelUtil.cpp' || echo './'`DindelUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-DindelRealignWindow.o `test -f 'DindelRealignWindow.cpp' || echo './'`DindelRealignWindow.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-DindelHMM.o `test -f 'DindelHMM.cpp' || echo './'`DindelHMM.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-OverlapHaplotypeBuilder.o `test -f 'OverlapHaplotypeBuilder.cpp' || echo './'`OverlapHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-StringHaplotypeBuilder.o `test -f 'StringHaplotypeBuilder.cpp' || echo './'`StringHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.o `test -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'`DeBruijnHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-VCFTester.o `test -f 'VCFTester.cpp' || echo './'`VCFTester.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-GraphCompare.o `test -f 'GraphCompare.cpp' || echo './'`GraphCompare.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o `test -f 'OverlapExtractorWithCorrection.cpp' || echo './'`OverlapExtractorWithCorrection.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp DindelUtil.cpp: In function 'DindelReturnCode DindelUtil::runDindelPairMatePair(const std::string&, const StringVector&, const StringVector&, const GraphCompareParameters&, std::ostream&, std::ostream&, std::ostream&, DindelReadReferenceAlignmentVector*)': DindelUtil.cpp:65:10: warning: variable 'has_complex_variant' set but not used [-Wunused-but-set-variable] 65 | bool has_complex_variant = false; | ^~~~~~~~~~~~~~~~~~~ DindelRealignWindow.cpp: In member function 'void DindelHaplotype::write(std::ostream&) const': DindelRealignWindow.cpp:762:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 762 | for (size_t x=0; x::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelRealignWindow.cpp:1037:115: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 1037 | for (std::list::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector&, std::unordered_map, std::__cxx11::list >&, const std::vector >&)': DindelRealignWindow.cpp:2589:12: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2589 | for (int h1=0;h1&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2743:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2743 | for (size_t x=0;x&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2906:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2906 | for (size_t x=0;x::pair(_U1&&, _U2&&) [with _U1 = int&; _U2 = DindelRealignWindowResult::Inference; typename std::enable_if<(std::_PCC::_MoveConstructiblePair<_U1, _U2>() && std::_PCC::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = const int; _T2 = DindelRealignWindowResult::Inference]' at /usr/include/c++/14/bits/stl_pair.h:882:35, inlined from 'void DindelRealignWindow::addCalledHaplotypeSingleRead(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)' at DindelRealignWindow.cpp:2774:147: DindelRealignWindow.h:637:15: warning: '.DindelRealignWindowResult::Inference::qual' is used uninitialized [-Wuninitialized] 637 | class Inference | ^~~~~~~~~ DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::addCalledHaplotypeSingleRead(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2774:146: note: '' declared here 2774 | result.hapIdxToInference.insert(DindelRealignWindowResult::HapIdxToInference::value_type(hapIdx,DindelRealignWindowResult::Inference())); | ^ In constructor 'DindelRealignWindowResult::Inference::Inference(DindelRealignWindowResult::Inference&&)', inlined from 'constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = int&; _U2 = DindelRealignWindowResult::Inference; typename std::enable_if<(std::_PCC::_MoveConstructiblePair<_U1, _U2>() && std::_PCC::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = const int; _T2 = DindelRealignWindowResult::Inference]' at /usr/include/c++/14/bits/stl_pair.h:882:35, inlined from 'void DindelRealignWindow::addCalledHaplotypeMatePairs(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)' at DindelRealignWindow.cpp:2633:228: DindelRealignWindow.h:637:15: warning: '.DindelRealignWindowResult::Inference::qual' is used uninitialized [-Wuninitialized] 637 | class Inference | ^~~~~~~~~ DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::addCalledHaplotypeMatePairs(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2633:227: note: '' declared here 2633 | std::pair hapit_pair = result.hapIdxToInference.insert(DindelRealignWindowResult::HapIdxToInference::value_type(hapIdx,DindelRealignWindowResult::Inference())); | ^ rm -f libgraphdiff.a ar cr libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o ranlib libgraphdiff.a make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' Making all in SGA make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SGA' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-sga.o `test -f 'sga.cpp' || echo './'`sga.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-index.o `test -f 'index.cpp' || echo './'`index.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-overlap.o `test -f 'overlap.cpp' || echo './'`overlap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-assemble.o `test -f 'assemble.cpp' || echo './'`assemble.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-correct.o `test -f 'correct.cpp' || echo './'`correct.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-oview.o `test -f 'oview.cpp' || echo './'`oview.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-preprocess.o `test -f 'preprocess.cpp' || echo './'`preprocess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-rmdup.o `test -f 'rmdup.cpp' || echo './'`rmdup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-merge.o `test -f 'merge.cpp' || echo './'`merge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-subgraph.o `test -f 'subgraph.cpp' || echo './'`subgraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-scaffold.o `test -f 'scaffold.cpp' || echo './'`scaffold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.cpp merge.cpp: In function 'void parseMergeOptions(int, char**)': merge.cpp:173:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 173 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ preprocess.cpp: In function 'void parsePreprocessOptions(int, char**)': preprocess.cpp:616:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 616 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ index.cpp: In function 'void parseIndexOptions(int, char**)': index.cpp:276:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 276 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.cpp oview.cpp: In function 'void parseOviewOptions(int, char**)': oview.cpp:202:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 202 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from ../Util/EncodedString.h:22, from ../SuffixTools/Occurrence.h:13, from ../SuffixTools/RLBWT.h:13, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTDiskConstruction.h:19, from index.cpp:18: ../Util/EncodedString.h: In instantiation of 'void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]': ../Util/EncodedString.h:43:18: required from 'EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]' 43 | _copy(other); | ~~~~~^~~~~~~ /usr/include/c++/14/bits/new_allocator.h:191:4: required from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]' 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:575:17: required from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]' 575 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc:117:30: required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >; reference = EncodedString&]' 117 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1301:21: required from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; value_type = EncodedString]' 1301 | { emplace_back(std::move(__x)); } | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ index.cpp:130:27: required from here 130 | readSequences.push_back(sr.seq.toString()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ scaffold2fasta.cpp: In function 'void parseScaffold2fastaOptions(int, char**)': scaffold2fasta.cpp:196:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 196 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ rmdup.cpp: In function 'void parseRmdupOptions(int, char**)': rmdup.cpp:348:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 348 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ overlap.cpp: In function 'void parseOverlapOptions(int, char**)': overlap.cpp:327:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 327 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ assemble.cpp: In function 'void parseAssembleOptions(int, char**)': assemble.cpp:234:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 234 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-walk.o `test -f 'walk.cpp' || echo './'`walk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.cpp scaffold.cpp: In function 'void parseScaffoldOptions(int, char**)': scaffold.cpp:189:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 189 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ correct.cpp: In function 'void parseCorrectOptions(int, char**)': correct.cpp:330:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 330 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.cpp subgraph.cpp: In function 'void parseSubgraphOptions(int, char**)': subgraph.cpp:169:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 169 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.cpp In file included from connect.cpp:15: connect.cpp: In function 'int connectMain(int, char**)': ../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ connect.cpp:297:17: note: in expansion of macro 'WARN_ONCE' 297 | WARN_ONCE("check orientation of result"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ connect.cpp:297:17: note: in expansion of macro 'WARN_ONCE' 297 | WARN_ONCE("check orientation of result"); | ^~~~~~~~~ connect.cpp: In function 'void parseConnectOptions(int, char**)': connect.cpp:465:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 465 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-fm-merge.o `test -f 'fm-merge.cpp' || echo './'`fm-merge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-gmap.o `test -f 'gmap.cpp' || echo './'`gmap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-filterBAM.o `test -f 'filterBAM.cpp' || echo './'`filterBAM.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-cluster.o `test -f 'cluster.cpp' || echo './'`cluster.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.cpp kmer-count.cpp: In function 'void parseKmerCountOptions(int, char**)': kmer-count.cpp:63:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 63 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ walk.cpp: In function 'void parseWalkOptions(int, char**)': walk.cpp:323:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 323 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ filter.cpp: In function 'void parseFilterOptions(int, char**)': filter.cpp:217:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 217 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ stats.cpp: In function 'void parseStatsOptions(int, char**)': stats.cpp:171:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 171 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.cpp fm-merge.cpp: In function 'void parseFMMergeOptions(int, char**)': fm-merge.cpp:164:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 164 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-graph-diff.o `test -f 'graph-diff.cpp' || echo './'`graph-diff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-graph-concordance.o `test -f 'graph-concordance.cpp' || echo './'`graph-concordance.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp gen-ssa.cpp: In function 'void parseGenSSAOptions(int, char**)': gen-ssa.cpp:108:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 108 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ gmap.cpp: In function 'void parseGmapOptions(int, char**)': gmap.cpp:303:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 303 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-preqc.o `test -f 'preqc.cpp' || echo './'`preqc.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-overlap-long.o `test -f 'overlap-long.cpp' || echo './'`overlap-long.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-variant-detectability.o `test -f 'variant-detectability.cpp' || echo './'`variant-detectability.cpp bwt2fa.cpp: In function 'void parseBWT2FAOptions(int, char**)': bwt2fa.cpp:96:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 96 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ filterBAM.cpp: In function 'void parseFilterBAMOptions(int, char**)': filterBAM.cpp:438:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 438 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.cpp cluster.cpp: In function 'void parseClusterOptions(int, char**)': cluster.cpp:292:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 292 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-somatic-variant-filters.o `test -f 'somatic-variant-filters.cpp' || echo './'`somatic-variant-filters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp variant-detectability.cpp: In function 'void parseVarDetectOptions(int, char**)': variant-detectability.cpp:205:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 205 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ overlap-long.cpp: In function 'void parseOverlapLongOptions(int, char**)': overlap-long.cpp:338:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 338 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ graph-diff.cpp: In function 'void parseGraphDiffOptions(int, char**)': graph-diff.cpp:493:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 493 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ graph-concordance.cpp: In function 'std::string reconstructHaplotype(const VCFRecord&, VariantRecordVector, const ReadTable&, const BWTIndexSet&, size_t)': graph-concordance.cpp:214:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 214 | if(end > chr.seq.length()) | ~~~~^~~~~~~~~~~~~~~~~~ graph-concordance.cpp: In function 'void parseGraphConcordanceOptions(int, char**)': graph-concordance.cpp:437:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 437 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from rewrite-evidence-bam.cpp:18: /usr//include/bamtools/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from rewrite-evidence-bam.cpp:10: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ rewrite-evidence-bam.cpp: In function 'void parseRewriteEvidenceBAMOptions(int, char**)': rewrite-evidence-bam.cpp:158:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 158 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ gapfill.cpp: In function 'void parseGapFillOptions(int, char**)': gapfill.cpp:148:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 148 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from ../Thirdparty/rapidjson/reader.h:7, from ../Thirdparty/rapidjson/document.h:4, from preqc.cpp:27: ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF8::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef170' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:170:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 170 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static rapidjson::UTF8::Ch rapidjson::UTF8::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef183' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:183:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 183 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF8::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef189' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:189:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 189 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF8::Put(OutputByteStream&, Ch)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef195' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:195:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 195 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16::Encode(OutputStream&, unsigned int)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef219' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:219:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 219 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF16::Decode(InputStream&, unsigned int*)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef234' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:234:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 234 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF16::Validate(InputStream&, OutputStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef252' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:252:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 252 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef253' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:253:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 253 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16LE::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef271' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:271:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 271 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16LE::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef278' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:278:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 278 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16LE::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef286' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:286:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 286 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16LE::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef292' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:292:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 292 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16BE::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef303' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:303:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 303 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16BE::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef310' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:310:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 310 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16BE::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef318' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:318:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 318 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16BE::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef324' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:324:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 324 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32::Encode(OutputStream&, unsigned int)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef348' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:348:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 348 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF32::Decode(InputStream&, unsigned int*)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef355' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:355:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 355 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF32::Validate(InputStream&, OutputStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef363' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:363:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 363 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32LE::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef375' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:375:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 375 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32LE::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef382' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:382:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 382 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32LE::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef392' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:392:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 392 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32LE::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef398' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:398:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 398 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32BE::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef411' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:411:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 411 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32BE::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef418' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:418:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 418 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32BE::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef428' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:428:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 428 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32BE::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef434' locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:434:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 434 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp preqc.cpp: In function 'void parsePreQCOptions(int, char**)': preqc.cpp:2090:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 2090 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ somatic-variant-filters.cpp: In function 'CoverageStats getVariantCoverage(BamTools::BamReader*, const VCFRecord&, const ReadTable*)': somatic-variant-filters.cpp:305:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 305 | std::random_shuffle(alignments.begin(), alignments.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from somatic-variant-filters.cpp:16: /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ somatic-variant-filters.cpp: In function 'void parseSomaticVariantFiltersOptions(int, char**)': somatic-variant-filters.cpp:794:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 794 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ haplotype-filter.cpp: In function 'std::vector simulateCoverageHaploid(double, size_t, size_t)': haplotype-filter.cpp:722:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 722 | std::random_shuffle(indices.begin(), indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from haplotype-filter.cpp:16: /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function 'std::vector simulateCoverageDiploid(double, size_t, size_t)': haplotype-filter.cpp:756:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 756 | std::random_shuffle(initial_indices.begin(), initial_indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function 'std::vector simulateCoverageHaploidNonUniform(std::vector, size_t, double&)': haplotype-filter.cpp:837:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 837 | std::random_shuffle(initial_indices.begin(), initial_indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function 'std::vector simulateCoverageDiploidNonUniform(std::vector, size_t, double&)': haplotype-filter.cpp:903:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 903 | std::random_shuffle(initial_indices.begin(), initial_indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function 'void parseHaplotypeFilterOptions(int, char**)': haplotype-filter.cpp:1066:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1066 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -fopenmp -L/usr//lib -L/usr//lib/bamtools -Wl,-z,relro -Wl,-z,now -o sga sga-sga.o sga-index.o sga-overlap.o sga-assemble.o sga-correct.o sga-oview.o sga-preprocess.o sga-rmdup.o sga-merge.o sga-subgraph.o sga-scaffold.o sga-scaffold2fasta.o sga-connect.o sga-walk.o sga-filter.o sga-kmer-count.o sga-stats.o sga-fm-merge.o sga-gmap.o sga-filterBAM.o sga-cluster.o sga-gen-ssa.o sga-bwt2fa.o sga-graph-diff.o sga-graph-concordance.o sga-gapfill.o sga-preqc.o sga-overlap-long.o sga-variant-detectability.o sga-rewrite-evidence-bam.o sga-somatic-variant-filters.o sga-haplotype-filter.o sga-OverlapCommon.o ../Scaffold/libscaffold.a ../GraphDiff/libgraphdiff.a ../StringGraph/libstringgraph.a ../Concurrency/libconcurrency.a ../Algorithm/libalgorithm.a ../SuffixTools/libsuffixtools.a ../Bigraph/libbigraph.a ../Util/libutil.a ../SQG/libsqg.a ../Thirdparty/libthirdparty.a -lz -lbamtools make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SGA' make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' make[1]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' dh_auto_test -O--sourcedirectory=src cd src && make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sga-0.10.15/src' Making check in bin make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/bin' Making check in Thirdparty make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' Making check in Util make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Util' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Util' Making check in SQG make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SQG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SQG' Making check in Bigraph make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' Making check in Algorithm make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' Making check in StringGraph make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' Making check in Concurrency make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' Making check in SuffixTools make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' Making check in Scaffold make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' Making check in GraphDiff make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' Making check in SGA make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SGA' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SGA' make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src' make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' make[1]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/sga-0.10.15' dh_auto_install cd src && make -j12 install DESTDIR=/build/reproducible-path/sga-0.10.15/debian/sga AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/sga-0.10.15/src' Making install in bin make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/bin' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/bin' /usr/bin/mkdir -p '/build/reproducible-path/sga-0.10.15/debian/sga/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c sga-bam2de sga-mergeDriver '/build/reproducible-path/sga-0.10.15/debian/sga/usr/bin' make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/bin' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/bin' Making install in Thirdparty make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Thirdparty' Making install in Util make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Util' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Util' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Util' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Util' Making install in SQG make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SQG' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SQG' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SQG' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SQG' Making install in Bigraph make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Bigraph' Making install in Algorithm make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Algorithm' Making install in StringGraph make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/StringGraph' Making install in Concurrency make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Concurrency' Making install in SuffixTools make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SuffixTools' Making install in Scaffold make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/Scaffold' Making install in GraphDiff make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/GraphDiff' Making install in SGA make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SGA' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src/SGA' /usr/bin/mkdir -p '/build/reproducible-path/sga-0.10.15/debian/sga/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c sga '/build/reproducible-path/sga-0.10.15/debian/sga/usr/bin' make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SGA' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src/SGA' make[3]: Entering directory '/build/reproducible-path/sga-0.10.15/src' make[4]: Entering directory '/build/reproducible-path/sga-0.10.15/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' make[3]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' make[2]: Leaving directory '/build/reproducible-path/sga-0.10.15/src' cp -a src/bin/sga-bam2de.pl debian/sga/usr/bin/sga-bam2de cp -a src/bin/sga-astat.py debian/sga/usr/bin/sga-astat make[1]: Leaving directory '/build/reproducible-path/sga-0.10.15' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/sga-0.10.15' dh_installexamples mkdir -p debian/sga/usr/share/doc/sga/examples sed -e 's?^\(SGA_BIN=sga\).*?\1?' \ -e 's?^.*/bin/sga-align?sga-align?' \ -e 's?^.*/bin/sga-bam2de.pl?sga-bam2de?' \ -e 's?^.*/bin/sga-astat.py?sga-astat?' \ src/examples/sga-celegans.sh > debian/sga/usr/share/doc/sga/examples/sga-celegans.sh make[1]: Leaving directory '/build/reproducible-path/sga-0.10.15' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/sga-0.10.15' dh_installman mkdir -p /build/reproducible-path/sga-0.10.15/debian/sga/usr/share/man/man1/ PATH=/usr/lib/abyss:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man \ --version-string="0.10.15" \ --no-info \ --name "Make a distance estimate file from a bam file of reads aligned to contigs" \ --output /build/reproducible-path/sga-0.10.15/debian/sga/usr/share/man/man1//sga-bam2de.1 \ /build/reproducible-path/sga-0.10.15/debian/sga/usr/bin/sga-bam2de help2man \ --no-info \ --version-string="0.10.15" \ --name="String Graph Assembler: de novo genome assembler that uses string graphs" \ --output /build/reproducible-path/sga-0.10.15/debian/sga/usr/share/man/man1//sga.1 \ /build/reproducible-path/sga-0.10.15/debian/sga/usr/bin/sga help2man \ --no-info\ --version-string="0.10.15" \ --name="generate sga merge commands from a list of files" \ --output /build/reproducible-path/sga-0.10.15/debian/sga/usr/share/man/man1//sga-mergeDriver.1 \ /build/reproducible-path/sga-0.10.15/debian/sga/usr/bin/sga-mergeDriver make[1]: Leaving directory '/build/reproducible-path/sga-0.10.15' dh_python3 -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sga-dbgsym' in '../sga-dbgsym_0.10.15-7_arm64.deb'. dpkg-deb: building package 'sga' in '../sga_0.10.15-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../sga_0.10.15-7_arm64.buildinfo dpkg-genchanges --build=binary -O../sga_0.10.15-7_arm64.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/3066102 and its subdirectories I: Current time: Thu Mar 19 00:02:14 -12 2026 I: pbuilder-time-stamp: 1773921734 Fri Feb 14 05:39:17 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Feb 14 05:39:17 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Feb 14 05:41:54 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Feb 14 05:41:54 UTC 2025 I: sga_0.10.15-7_arm64.changes: Format: 1.8 Date: Fri, 17 Sep 2021 15:56:21 +0200 Source: sga Binary: sga sga-dbgsym Architecture: arm64 Version: 0.10.15-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: sga - de novo genome assembler that uses string graphs Changes: sga (0.10.15-7) unstable; urgency=medium . * Fix watchfile to detect new versions on github (routine-update) * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Include ${perl:Depends} Checksums-Sha1: 154eb4465af61d5903bc238e590a69ded703a586 12683540 sga-dbgsym_0.10.15-7_arm64.deb ccc6b8ef381dabe480dfe1067e2569b97139b74f 8789 sga_0.10.15-7_arm64.buildinfo 7888c2b9376d0a8a05ec349e1735f022e34a9eb1 628416 sga_0.10.15-7_arm64.deb Checksums-Sha256: 9cf22d11514e22db4f49beac70125a2b84df6886f081f798e3f3c7d7d13bcda7 12683540 sga-dbgsym_0.10.15-7_arm64.deb c61d2b3654f27114f561c5fd2bd7e952311331c3f8ec3a060db9ceef889031d3 8789 sga_0.10.15-7_arm64.buildinfo d11b58b73969768c057c355b4959e4069379c8d1d784308328987d38dd5d01c7 628416 sga_0.10.15-7_arm64.deb Files: d3a3617650b0f0e56d12efd22b8ccfe4 12683540 debug optional sga-dbgsym_0.10.15-7_arm64.deb 752414236335c78f2dbc2561b0b1311f 8789 science optional sga_0.10.15-7_arm64.buildinfo 89d9b04c47a21f44ca0bbfb79cfbae2a 628416 science optional sga_0.10.15-7_arm64.deb Fri Feb 14 05:41:56 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_6-79447.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TlCvmfAt/sga_0.10.15-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TlCvmfAt/sga_0.10.15-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TlCvmfAt/sga_0.10.15-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TlCvmfAt/b1/sga_0.10.15-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TlCvmfAt/b2/sga_0.10.15-7_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 224ms CPU time consumed: 225ms Fri Feb 14 05:41:56 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 14 05:41:56 UTC 2025 I: sga from trixie built successfully and reproducibly on arm64. Fri Feb 14 05:41:57 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 14 05:41:58 UTC 2025 I: Submitting 12K b1/sga_0.10.15-7_arm64.buildinfo.asc Fri Feb 14 05:41:58 UTC 2025 I: Submitting 12K b2/sga_0.10.15-7_arm64.buildinfo.asc Fri Feb 14 05:42:00 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 14 05:42:00 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 14 05:42:00 UTC 2025 I: Removing signed sga_0.10.15-7_arm64.buildinfo.asc files: removed './b1/sga_0.10.15-7_arm64.buildinfo.asc' removed './b2/sga_0.10.15-7_arm64.buildinfo.asc'