Sun Oct 20 16:40:23 UTC 2024 I: starting to build sga/trixie/amd64 on jenkins on '2024-10-20 16:40' Sun Oct 20 16:40:23 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_32/23400/console.log Sun Oct 20 16:40:23 UTC 2024 I: Downloading source for trixie/sga=0.10.15-7 --2024-10-20 16:40:24-- 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% 284M=0s 2024-10-20 16:40:24 (284 MB/s) - ‘sga_0.10.15-7.dsc’ saved [2084/2084] Sun Oct 20 16:40:24 UTC 2024 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----- Sun Oct 20 16:40:24 UTC 2024 I: Checking whether the package is not for us Sun Oct 20 16:40:24 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Sun Oct 20 16:40:24 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Sun Oct 20 16:42:41 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 22 11:03:21 -12 2025 I: pbuilder-time-stamp: 1763852601 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 gpgv: Signature made Fri Sep 17 14:05:16 2021 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sga_0.10.15-7.dsc: no acceptable signature found 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/3530899/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6d909ea58f994fb9b8cbe66f6faad47d' 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='3530899' 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.EQNTZXUS/pbuilderrc_UCNc --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.EQNTZXUS/b1 --logfile b1/build.log sga_0.10.15-7.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3530899/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: amd64 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 ... 19799 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} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{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} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} libldap-2.5-0{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} libnsl2{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} libpython3.12-minimal{a} libpython3.12-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} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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-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} python3.12{a} python3.12-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, 153 newly installed, 0 to remove and 0 not upgraded. Need to get 56.5 MB of archives. After unpacking 219 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libcdt5 amd64 2.42.4-2 [40.2 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libcgraph6 amd64 2.42.4-2 [64.0 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.9.1-1 [1864 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.4.3-1 [551 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 librav1e0.7 amd64 0.7.1-7+b1 [921 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0.1888.20240710-3 [170 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.18.2-2 [10.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.18.2-2 [14.2 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.18.2-2 [312 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.1-1 [1499 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-12 [125 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2 [157 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [223 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [54.4 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [35.2 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libpathplan4 amd64 2.42.4-2 [42.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libgvc6 amd64 2.42.4-2 [686 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgvpr2 amd64 2.42.4-2 [192 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 liblab-gamut1 amd64 2.42.4-2 [198 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 graphviz amd64 2.42.4-2 [618 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-ruffus all 2.8.4-5 [151 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Fetched 56.5 MB in 1s (74.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19799 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (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 ... 20133 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21205 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40.2-9_amd64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../015-autopoint_0.22.5-2_all.deb ... 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Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up dh-python (6.20240824) ... Setting up libheif-plugin-dav1d:amd64 (1.18.2-2) ... Setting up libheif1:amd64 (1.18.2-2) ... Setting up libgd3:amd64 (2.3.3-12) ... Setting up libgvc6 (2.42.4-2) ... Setting up graphviz (2.42.4-2) ... Setting up libheif-plugin-libde265:amd64 (1.18.2-2) ... Setting up python3-ruffus (2.8.4-5) ... /usr/lib/python3/dist-packages/ruffus/cmdline.py:668: SyntaxWarning: invalid escape sequence '\d' """ /usr/lib/python3/dist-packages/ruffus/combinatorics.py:26: SyntaxWarning: invalid escape sequence '\.' """ /usr/lib/python3/dist-packages/ruffus/parse_old_style_ruffus.py:178: SyntaxWarning: invalid escape sequence '\s' func_re = re.compile("^\s*def.*\(") /usr/lib/python3/dist-packages/ruffus/parse_old_style_ruffus.py:195: SyntaxWarning: invalid escape sequence '\s' decorator_re = re.compile("^\s*@") /usr/lib/python3/dist-packages/ruffus/parse_old_style_ruffus.py:196: SyntaxWarning: invalid escape sequence '\s' no_white_space_re = re.compile("^[^#\s]") /usr/lib/python3/dist-packages/ruffus/proxy_logger.py:26: SyntaxWarning: invalid escape sequence '\ ' """ /usr/lib/python3/dist-packages/ruffus/proxy_logger.py:323: SyntaxWarning: invalid escape sequence '\ ' """ /usr/lib/python3/dist-packages/ruffus/ruffus_utility.py:502: SyntaxWarning: invalid escape sequence '\d' """ /usr/lib/python3/dist-packages/ruffus/test/draw_specified_dependency_tree.py:112: SyntaxWarning: invalid escape sequence '\[' attributes = re.compile("\[.+\]") /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:388: SyntaxWarning: invalid escape sequence '\[' '\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:391: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:463: SyntaxWarning: invalid escape sequence '\[' '\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:465: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:489: SyntaxWarning: invalid escape sequence '\[' '\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:492: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:516: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:518: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:541: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:544: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:568: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:570: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:593: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_combinatorics.py:596: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:800: SyntaxWarning: invalid escape sequence '\w' task.formatter("/(?P\w+).test$"), /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:1592: SyntaxWarning: invalid escape sequence '\w' task.formatter("(?:.+/)?(?P\w+)\.(.+)"), /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:1594: SyntaxWarning: invalid escape sequence '\w' task.formatter("(?:.+/)?(?P\w+)\.(test2)"), /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:1633: SyntaxWarning: invalid escape sequence '\w' paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter("(?:.+/)?(?P\w+)\.(.+)"), /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:1635: SyntaxWarning: invalid escape sequence '\w' "/e.ignore"], task.formatter("(?:.+/)?(?P\w+)\.(test2)"), /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:1652: SyntaxWarning: invalid escape sequence '\w' paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter("(?:.+/)?(?P\w+)\.(.+)"), /usr/lib/python3/dist-packages/ruffus/test/test_file_name_parameters.py:1654: SyntaxWarning: invalid escape sequence '\w' "/e.ignore"], task.formatter("(?:.+/)?(?P\w+)\.(test2)"), /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:400: SyntaxWarning: invalid escape sequence '\[' '\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:403: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:474: SyntaxWarning: invalid escape sequence '\[' '\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:476: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:500: SyntaxWarning: invalid escape sequence '\[' '\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:503: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:527: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:529: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:552: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:555: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:579: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:581: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:604: SyntaxWarning: invalid escape sequence '\[' self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_combinatorics.py:607: SyntaxWarning: invalid escape sequence '\]' '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:310: SyntaxWarning: invalid escape sequence '\[' 'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:352: SyntaxWarning: invalid escape sequence '\[' 'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:370: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:375: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:409: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:414: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:426: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:431: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:444: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_newstyle_regex_error_messages.py:449: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:302: SyntaxWarning: invalid escape sequence '\[' 'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:344: SyntaxWarning: invalid escape sequence '\[' 'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:362: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:367: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:401: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:406: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:418: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:423: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:436: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_regex_error_messages.py:441: SyntaxWarning: invalid escape sequence '\(' "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", /usr/lib/python3/dist-packages/ruffus/test/test_ruffus_utility.py:511: SyntaxWarning: invalid escape sequence '\.' regex_str = "([a-z]+)\.([a-z]+)\.([a-z]+)\.([a-z]+)" Processing triggers for libc-bin (2.40-3) ... 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 amd64 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=x86_64-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/x86_64-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 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 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 -j42 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 cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.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"); | ^~~~~~~~~ rm -f libutil.a ar cru 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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp rm -f libsqg.a ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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:222:11: 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]' 222 | _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 cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.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") | ^~~~~~~~~ rm -f libalgorithm.a ar cru 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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 cru 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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp rm -f libconcurrency.a ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.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:569:17: required from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]' 569 | __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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 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; | ^~~~~ rm -f libsuffixtools.a ar cru 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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 cru 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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp 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; | ^~~ 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; | ^~~~~~~~~~~~~~~~~~~ DeBruijnHaplotypeBuilder.cpp: In member function 'Vertex* DeBruijnHaplotypeBuilder::extendUnambiguously(Vertex*, StringGraph*, EdgeDir, size_t, size_t)': DeBruijnHaplotypeBuilder.cpp:227:16: warning: variable 'ext_count' set but not used [-Wunused-but-set-variable] 227 | size_t ext_count = 0; | ^~~~~~~~~ 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 cru 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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.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 -fcf-protection -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.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 -fcf-protection -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 -fcf-protection -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.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 -fcf-protection -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.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 -fcf-protection -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.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 -fcf-protection -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o sga-variant-detectability.o `test -f 'variant-detectability.cpp' || echo './'`variant-detectability.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 -fcf-protection -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.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 -fcf-protection -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 -fcf-protection -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.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 -fcf-protection -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp 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 | ^~~~~~~~~~~~~~~ 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:569:17: required from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]' 569 | __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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~ 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:4491:5: note: declared here 4491 | 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:4491:5: note: declared here 4491 | 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:4491:5: note: declared here 4491 | 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:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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"); | ^~~~~~~~~ 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()) | ~~~~^~~~~~~~~~~~~~~~~~ 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:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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 -fcf-protection -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 -j42 check "TESTSUITEFLAGS=-j42 --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 -j42 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' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/sga-0.10.15/debian/sga/usr/bin' /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' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/sga-0.10.15/debian/sga/usr/bin' /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 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' in '../sga_0.10.15-7_amd64.deb'. dpkg-deb: building package 'sga-dbgsym' in '../sga-dbgsym_0.10.15-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../sga_0.10.15-7_amd64.buildinfo dpkg-genchanges --build=binary -O../sga_0.10.15-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/3530899 and its subdirectories I: Current time: Sat Nov 22 11:05:36 -12 2025 I: pbuilder-time-stamp: 1763852736 Sun Oct 20 16:42:42 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sun Oct 20 16:42:42 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sun Oct 20 17:08:29 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sun Oct 20 17:08:30 UTC 2024 I: sga_0.10.15-7_amd64.changes: Format: 1.8 Date: Fri, 17 Sep 2021 15:56:21 +0200 Source: sga Binary: sga sga-dbgsym Architecture: amd64 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: d71f16c895e26a5f023952a1cbf8636cead97c22 15742164 sga-dbgsym_0.10.15-7_amd64.deb 3164f8b11490fea21f0415bcb84ae75f5ad0384d 8843 sga_0.10.15-7_amd64.buildinfo f51ccfcda4b878862bb2b55ec936f2afbe8ef4b4 901768 sga_0.10.15-7_amd64.deb Checksums-Sha256: af2c27f02972c66bfd5f00b9ba096a96215f7cab7d1ea47b51e08aac271e6c7c 15742164 sga-dbgsym_0.10.15-7_amd64.deb 1b59eebada6925f5815ca8fe70b769ccf0f90917752993bb51245a71e6c69fe7 8843 sga_0.10.15-7_amd64.buildinfo c52ef86748fb07f81d3c393466faf2b8894ee988980794a802f2ccc1c4ca57dc 901768 sga_0.10.15-7_amd64.deb Files: f560c094f367d0501be2c4cae64bd97f 15742164 debug optional sga-dbgsym_0.10.15-7_amd64.deb 73956fd456810e00040bccfac3efdd26 8843 science optional sga_0.10.15-7_amd64.buildinfo bbdc30f3e014b7d95421e848f8172408 901768 science optional sga_0.10.15-7_amd64.deb Sun Oct 20 17:08:31 UTC 2024 I: diffoscope 281 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_32-23400.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EQNTZXUS/sga_0.10.15-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EQNTZXUS/sga_0.10.15-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EQNTZXUS/sga_0.10.15-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EQNTZXUS/b1/sga_0.10.15-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.EQNTZXUS/b2/sga_0.10.15-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.627s) 0.627s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.197s) 0.197s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.056s CPU time consumed: 1.051s Sun Oct 20 17:08:33 UTC 2024 I: diffoscope 281 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 20 17:08:33 UTC 2024 I: sga from trixie built successfully and reproducibly on amd64. Sun Oct 20 17:08:35 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Oct 20 17:08:35 UTC 2024 I: Submitting 12K b1/sga_0.10.15-7_amd64.buildinfo.asc Sun Oct 20 17:08:35 UTC 2024 I: Submitting 12K b2/sga_0.10.15-7_amd64.buildinfo.asc Sun Oct 20 17:08:36 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Oct 20 17:08:36 UTC 2024 I: Done submitting .buildinfo files. Sun Oct 20 17:08:36 UTC 2024 I: Removing signed sga_0.10.15-7_amd64.buildinfo.asc files: removed './b1/sga_0.10.15-7_amd64.buildinfo.asc' removed './b2/sga_0.10.15-7_amd64.buildinfo.asc'