Running as unit: rb-build-arm64_7-41826.service ==================================================================================== Sun Oct 27 12:03:32 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_7) on jenkins, called using "codethink02-arm64 codethink03-arm64" as arguments. Sun Oct 27 12:03:32 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-LG2eRXz7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Oct 27 12:03:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Sun Oct 27 12:03:32 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Q9KQmX' Sun Oct 27 12:03:33 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sun Oct 27 12:03:33 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Yi4kcy' ok, let's check if velvet is building anywhere yet… ok, velvet is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of velvet in unstable on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Sun Oct 27 12:03:54 UTC 2024 I: starting to build velvet/unstable/arm64 on jenkins on '2024-10-27 12:03' Sun Oct 27 12:03:54 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/41826/console.log 1730030634 arm64 unstable velvet Sun Oct 27 12:03:54 UTC 2024 I: Downloading source for unstable/velvet=1.2.10+dfsg1-9 --2024-10-27 12:03:55-- http://deb.debian.org/debian/pool/main/v/velvet/velvet_1.2.10%2bdfsg1-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2393 (2.3K) [text/prs.lines.tag] Saving to: ‘velvet_1.2.10+dfsg1-9.dsc’ 0K .. 100% 293M=0s 2024-10-27 12:03:55 (293 MB/s) - ‘velvet_1.2.10+dfsg1-9.dsc’ saved [2393/2393] --2024-10-27 12:03:55-- http://deb.debian.org/debian/pool/main/v/velvet/velvet_1.2.10%2bdfsg1-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2393 (2.3K) [text/prs.lines.tag] Saving to: ‘velvet_1.2.10+dfsg1-9.dsc’ 0K .. 100% 293M=0s 2024-10-27 12:03:55 (293 MB/s) - ‘velvet_1.2.10+dfsg1-9.dsc’ saved [2393/2393] Sun Oct 27 12:03:55 UTC 2024 I: velvet_1.2.10+dfsg1-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: velvet Binary: velvet, velvet-long, velvet-example, velvet-tests Architecture: any all Version: 1.2.10+dfsg1-9 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/dzerbino/velvet Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/velvet Vcs-Git: https://salsa.debian.org/med-team/velvet.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended Package-List: velvet deb science optional arch=any velvet-example deb science optional arch=all velvet-long deb science optional arch=any velvet-tests deb science optional arch=all Checksums-Sha1: f5ade530e902bdf69532648429a91c00f3a1ad2d 13630488 velvet_1.2.10+dfsg1.orig.tar.xz a90ae2c99b8e907d21ea487acced5450df59e5ec 18476 velvet_1.2.10+dfsg1-9.debian.tar.xz Checksums-Sha256: 368d760ad56ffa010a2ae72b25d46680ecb7ad8cc573cf6c389848c87b32ee26 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 6d34641dd5a1fec20bb47508d3e2e045cd06a0e73dbeda44e38c90be0b135183 18476 velvet_1.2.10+dfsg1-9.debian.tar.xz Files: 7a58a6d75cdc8b89d1c605033050bbcf 13630488 velvet_1.2.10+dfsg1.orig.tar.xz a40a683daca2441b5ded8972fbe1508b 18476 velvet_1.2.10+dfsg1-9.debian.tar.xz Dgit: 89cc29c026c11e5aeb7087d5bc0b483a4b20195c debian archive/debian/1.2.10+dfsg1-9 https://git.dgit.debian.org/velvet -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmazSnAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrtrw/9Fix53xMaAsOS+/+ayiJu1CQ9ZzQk dTHcW7I9CoaGIcAW5xv2ftijQyIflHZncoSCPtGRFWEGI4hvBEhPxwcdOqMKOxSx Si3IDGXmq+Oreo1spqUwC3/U1yXS71UFAs9znfTBhG0h8BxZ6OS6glj6STyh2NEl dITOOFVzNRr9jrM80v7vydF0dv4LJoWsMdE+aQgNBsxQph60Bsm3+nriKclv5B2U kamA3uqbCUBuxeXoPxMmrXraRhE6VsKqTsp4VVIcKm5OnQ1DLG5iENMYYyQ8yKdK WVki6GereTkzO5Dh5CzJrDDofiXrpepr7O2zGvIEKnmlStp3icEOmb6X6VgddaS6 l8WSlg3QbF/hayDmG/lvUEk4uxuI3ERA08l6riodrJMvKSRBAnH2WnOxqt1ljjLE VXE87J0Ig/q1fgLstSPEoJexWZwy3UR0BfegzRlUbS6rK/CyJyYQB12ABiiLtIwO XGSZcJq7OtywDX44CpsIMgfc/dOzMhqAuIIzAMIEjh53ldczkfUbXlkgxB4Prwpa 0VpNlPUCWjpdnL/zdTIRYyQy69JshmuPlXE+lmqVVOCBb0tWz6OxJaK5aAlGc9yK DYwM5SBTrHRgieDJBgqibjJkX1dLlRZvRLgiGjCknKCeFx7jkKPhNakQrFO4+XU+ yyGx3WwCjhKdt78= =KJVv -----END PGP SIGNATURE----- Sun Oct 27 12:03:55 UTC 2024 I: Checking whether the package is not for us Sun Oct 27 12:03:55 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sun Oct 27 12:03:55 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sun Oct 27 12:03:55 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Sun Oct 27 12:03:55 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-WdVhMQ' ==================================================================================== Sun Oct 27 12:03:57 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 velvet unstable /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE 1.2.10+dfsg1-9" as arguments. Sun Oct 27 12:03:57 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-gyKG8FC4" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Oct 27 12:03:57 UTC 2024 I: Downloading source for unstable/velvet=1.2.10+dfsg1-9 Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.7 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (dsc) [2393 B] Get:2 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (tar) [13.6 MB] Get:3 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (diff) [18.5 kB] Fetched 13.7 MB in 1s (23.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.7 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (dsc) [2393 B] Get:2 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (tar) [13.6 MB] Get:3 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (diff) [18.5 kB] Fetched 13.7 MB in 1s (23.8 MB/s) Download complete and in download only mode ============================================================================= Building velvet in unstable on arm64 on codethink02-arm64 now. Date: Sun Oct 27 12:03:58 GMT 2024 Date UTC: Sun Oct 27 12:03:58 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 27 00:03:58 -12 2024 I: pbuilder-time-stamp: 1730030638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [velvet_1.2.10+dfsg1-9.dsc] I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz] I: copying [./velvet_1.2.10+dfsg1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Aug 7 10:20:32 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-9.dsc: no acceptable signature found dpkg-source: info: extracting velvet in velvet-1.2.10+dfsg1 dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2865984/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='09a67f08ce4e49b8b58571bb55c491e4' 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='2865984' 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.p5QOSgFE/pbuilderrc_4fr1 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1 --logfile b1/build.log velvet_1.2.10+dfsg1-9.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2865984/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20056 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended 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-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu72{a} libkpathsea6{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libsm6{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} ucf{a} x11-common{a} xdg-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dvisvgm libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 74.5 MB of archives. After unpacking 244 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-4 [153 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-3 [34.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 60 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b1 [23.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-4 [47.9 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-4 [60.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1 [300 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-4 [106 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-4 [7373 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20240829-2 [22.7 MB] Get: 77 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Fetched 74.5 MB in 0s (216 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 20056 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_arm64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../10-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-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 .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../30-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../31-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../32-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../33-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../34-libbrotli1_1.1.0-2+b4_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b4) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../35-libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../36-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../37-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../38-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../39-libpixman-1-0_0.42.2-1+b1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.42.2-1+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../40-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../41-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../42-libxcb1_1.17.0-2_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../43-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../44-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../45-libxcb-render0_1.17.0-2_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../46-libxcb-shm0_1.17.0-2_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../47-libxext6_2%3a1.3.4-1+b2_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../48-libxrender1_1%3a0.9.10-1.1+b1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../49-libcairo2_1.18.2-2_arm64.deb ... Unpacking libcairo2:arm64 (1.18.2-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../50-libglib2.0-0t64_2.82.2-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.2-2) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../51-libgraphite2-3_1.3.14-2_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../52-libharfbuzz0b_10.0.1-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../53-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../54-libice6_2%3a1.0.10-1+b1_arm64.deb ... Unpacking libice6:arm64 (2:1.0.10-1+b1) ... Selecting previously unselected package libkpathsea6:arm64. Preparing to unpack .../55-libkpathsea6_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libmpfi0:arm64. Preparing to unpack .../56-libmpfi0_1.5.4+ds-3_arm64.deb ... Unpacking libmpfi0:arm64 (1.5.4+ds-3) ... Selecting previously unselected package libpaper1:arm64. Preparing to unpack .../57-libpaper1_1.1.29+b1_arm64.deb ... Unpacking libpaper1:arm64 (1.1.29+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../58-libpaper-utils_1.1.29+b1_arm64.deb ... Unpacking libpaper-utils (1.1.29+b1) ... Selecting previously unselected package libpotrace0:arm64. Preparing to unpack .../59-libpotrace0_1.16-2+b1_arm64.deb ... Unpacking libpotrace0:arm64 (1.16-2+b1) ... Selecting previously unselected package libptexenc1:arm64. Preparing to unpack .../60-libptexenc1_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../61-libsm6_2%3a1.2.3-1+b1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.3-1+b1) ... Selecting previously unselected package libsynctex2:arm64. Preparing to unpack .../62-libsynctex2_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libteckit0:arm64. Preparing to unpack .../63-libteckit0_2.5.12+ds1-1_arm64.deb ... Unpacking libteckit0:arm64 (2.5.12+ds1-1) ... Selecting previously unselected package libtexlua53-5:arm64. Preparing to unpack .../64-libtexlua53-5_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../65-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../66-libxmu6_2%3a1.1.3-3+b2_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.3-3+b2) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../67-libxpm4_1%3a3.5.17-1+b1_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.17-1+b1) ... Selecting previously unselected package libxaw7:arm64. Preparing to unpack .../68-libxaw7_2%3a1.0.14-1+b2_arm64.deb ... Unpacking libxaw7:arm64 (2:1.0.14-1+b2) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../69-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libzzip-0-13t64:arm64. Preparing to unpack .../70-libzzip-0-13t64_0.13.72+dfsg.1-1.3_arm64.deb ... Unpacking libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Selecting previously unselected package t1utils. Preparing to unpack .../71-t1utils_1.41-4_arm64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package tex-common. Preparing to unpack .../72-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../73-texlive-binaries_2024.20240313.70630+ds-4_arm64.deb ... Unpacking texlive-binaries (2024.20240313.70630+ds-4) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../74-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package texlive-base. Preparing to unpack .../75-texlive-base_2024.20240829-2_all.deb ... Unpacking texlive-base (2024.20240829-2) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../76-texlive-latex-base_2024.20240829-2_all.deb ... Unpacking texlive-latex-base (2024.20240829-2) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../77-texlive-latex-recommended_2024.20240829-2_all.deb ... Unpacking texlive-latex-recommended (2024.20240829-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../78-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:arm64 (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:arm64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:arm64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-4) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-4) ... Setting up libpotrace0:arm64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up gettext (0.22.5-2) ... Setting up libxpm4:arm64 (1:3.5.17-1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:arm64 (2024.20240313.70630+ds-4) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up libpaper1:arm64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libxmu6:arm64 (2:1.1.3-3+b2) ... Setting up debhelper (13.20) ... Setting up libxaw7:arm64 (2:1.0.14-1+b2) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240829-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up texlive-latex-base (2024.20240829-2) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 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/velvet-1.2.10+dfsg1/ && 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 > ../velvet_1.2.10+dfsg1-9_source.changes dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory rm: cannot remove './velvet*': No such file or directory make[2]: [Makefile:45: clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm -rf zlib rm -rf third-party rm -rf debian.upstream rm -f *.pdf find -name '._*' -delete rm -rf contrib/MetaVelvet* rm -rf contrib/VelvetOptimiser* make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' touch zlib #Make _long version dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_long ; mv velvetg velvetg_long #Make _63 kmer version dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_63 ; mv velvetg velvetg_63 #And also one with both options dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_63_long ; mv velvetg velvetg_63_long #Make _127 kmer version dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_127 ; mv velvetg velvetg_127 #And also one with both options dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_127_long ; mv velvetg velvetg_127_long touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Manual.aux. (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) No file Manual.toc. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 331. Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 354. LaTeX Warning: Reference `sec:kmercov' on page 8 undefined on input line 358. LaTeX Warning: Reference `sec:expcov' on page 8 undefined on input line 358. Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [8] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] LaTeX Warning: Reference `sec:hashing' on page 9 undefined on input line 377. LaTeX Warning: Reference `sec:kmercov' on page 9 undefined on input line 379. LaTeX Warning: Reference `sec:pairedformat' on page 9 undefined on input line 3 95. Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [9] [10] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:amos' on page 11 undefined on input line 455. Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 11 undefined on input line 470. Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set LaTeX Warning: Reference `sec:paper' on page 11 undefined on input line 499. [11] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [12] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [13] LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 593. LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 605. Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 615. [14] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 642. Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 683 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 695. LaTeX Warning: Reference `sec:kmercov' on page 16 undefined on input line 695. [16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /build/reproducible-path/velvet-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on Manual.pdf (21 pages, 432098 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./Manual.out ) (./Manual.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] [6] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov [15] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [16] [17] [18 <./Suis_plot_1.pdf>] [19 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [20] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [21] [22] (./Manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Manual.pdf (22 pages, 440025 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 145--145 [] \OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_sequ ences.fa[] [5] (./Columbus_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /build/reproducible-path/velvet-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 88603 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_auto_test -O--no-parallel make -j1 test make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[1]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:49: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] 1060 | RefInfo refElem; | ^~~~~~~ src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from src/passageMarker.c:22: In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:291:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:288:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:298:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:296:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ In file included from /usr/include/stdio.h:970, from src/readSet.c:22: In function 'snprintf', inlined from 'addMapping' at src/readSet.c:753:4, inlined from 'readCigar' at src/readSet.c:799:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 786 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) { | ~~~~~~~^~~~~~ In function 'snprintf', inlined from 'addMapping' at src/readSet.c:751:4, inlined from 'readCigar' at src/readSet.c:799:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 786 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) { | ~~~~~~~^~~~~~ src/readSet.c: In function 'importReadSet': src/readSet.c:1616:25: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 1616 | strncpy(sequence + bpCount, line, lineLength); | ^ src/readSet.c:1615:38: note: length computed here 1615 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:314:33: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] 314 | RefInfo refElem; | ^~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:414:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 414 | if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file)) | ^~ src/preGraphConstruction.c:416:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 416 | seqReadInfo->m_pFile = file; | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ src/kmer.c: At top level: src/kmer.c:31:22: warning: 'charLeftFilter' defined but not used [-Wunused-const-variable=] 31 | static const uint8_t charLeftFilter = (uint8_t) 3 << 6; | ^~~~~~~~~~~~~~ src/kmer.c:30:23: warning: 'intLeftFilter' defined but not used [-Wunused-const-variable=] 30 | static const uint16_t intLeftFilter = (uint16_t) 3 << 14; | ^~~~~~~~~~~~~ src/kmer.c:29:23: warning: 'longLeftFilter' defined but not used [-Wunused-const-variable=] 29 | static const uint32_t longLeftFilter = (uint32_t) 3 << 30; | ^~~~~~~~~~~~~~ src/kmer.c:28:23: warning: 'longLongLeftFilter' defined but not used [-Wunused-const-variable=] 28 | static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; | ^~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'pcloseNoStderr': src/autoOpen.c:49:13: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int rc, status; | ^~ src/autoOpen.c: At top level: src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] 56 | static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL}; | ^~~~~ src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cd tests && ./run-tests.sh [Sun Oct 27 12:06:58 2024] Running Velvet Test Suite [Sun Oct 27 12:06:58 2024] Found ../velveth, ok [Sun Oct 27 12:06:58 2024] Found ../velvetg, ok [Sun Oct 27 12:06:58 2024] Found Sequences.31, ok [Sun Oct 27 12:06:58 2024] Found Roadmaps.31, ok [Sun Oct 27 12:06:58 2024] Found read1.fq.gz, ok [Sun Oct 27 12:06:58 2024] Found read2.fq.gz, ok [Sun Oct 27 12:06:58 2024] Found reads.fq.gz, ok [Sun Oct 27 12:06:58 2024] Found read1.fa.gz, ok [Sun Oct 27 12:06:58 2024] Found read2.fa.gz, ok [Sun Oct 27 12:06:58 2024] Found reads.fa.gz, ok [Sun Oct 27 12:06:58 2024] making test folder: velvet.test.UFjyu8 [Sun Oct 27 12:06:58 2024] running test 1 of 5: fasta_eq_fastq_ascii.t [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] passed test 1 [Sun Oct 27 12:07:00 2024] running test 2 of 5: fasta_eq_fastq_binary.t [Sun Oct 27 12:07:01 2024] ok [Sun Oct 27 12:07:01 2024] ok [Sun Oct 27 12:07:01 2024] passed test 2 [Sun Oct 27 12:07:01 2024] running test 3 of 5: fmt_auto_mode.t [Sun Oct 27 12:07:03 2024] ok [Sun Oct 27 12:07:03 2024] ok [Sun Oct 27 12:07:03 2024] passed test 3 [Sun Oct 27 12:07:03 2024] running test 4 of 5: interleaved_eq_separate.t [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] passed test 4 [Sun Oct 27 12:07:07 2024] running test 5 of 5: mismatched_separates.t [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] passed test 5 [Sun Oct 27 12:07:07 2024] removing test folder: velvet.test.UFjyu8 [Sun Oct 27 12:07:07 2024] passed all 5 tests [Sun Oct 27 12:07:07 2024] hooray! make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel dh_install -O--no-parallel dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_installexamples -i xz -6 debian/velvet-example/usr/share/doc/velvet/examples/* sed -i 's?=\.\./velvet?=/usr/bin/velvet?' debian/velvet-tests/usr/share/doc/velvet/tests/run-tests.functions make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_compress -X.pdf -X.c -X.pl -X.h -X.xz make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-9_all.deb'. dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-9_all.deb'. dpkg-genbuildinfo --build=binary -O../velvet_1.2.10+dfsg1-9_arm64.buildinfo dpkg-genchanges --build=binary -O../velvet_1.2.10+dfsg1-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2865984 and its subdirectories I: Current time: Sun Oct 27 00:07:39 -12 2024 I: pbuilder-time-stamp: 1730030859 Sun Oct 27 12:07:39 UTC 2024 I: Signing ./b1/velvet_1.2.10+dfsg1-9_arm64.buildinfo as velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc Sun Oct 27 12:07:40 UTC 2024 I: Signed ./b1/velvet_1.2.10+dfsg1-9_arm64.buildinfo as ./b1/velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc Sun Oct 27 12:07:40 UTC 2024 - build #1 for velvet/unstable/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Sun Oct 27 12:07:40 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-gyKG8FC4, removing. /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Oct 27 12:07 b1 drwxr-xr-x 2 jenkins jenkins 4096 Oct 27 12:03 b2 -rw------- 1 jenkins jenkins 3532 Oct 27 12:03 rbuildlog.o4wvCsB -rw-r--r-- 1 jenkins jenkins 2393 Aug 7 10:31 velvet_1.2.10+dfsg1-9.dsc /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1: total 18016 -rw-r--r-- 1 jenkins jenkins 324786 Oct 27 12:07 build.log -rw-r--r-- 1 jenkins jenkins 990736 Oct 27 12:07 velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 3381368 Oct 27 12:07 velvet-example_1.2.10+dfsg1-9_all.deb -rw-r--r-- 1 jenkins jenkins 2078100 Oct 27 12:07 velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 198824 Oct 27 12:07 velvet-long_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 10748728 Oct 27 12:07 velvet-tests_1.2.10+dfsg1-9_all.deb -rw-r--r-- 1 jenkins jenkins 18476 Oct 27 12:07 velvet_1.2.10+dfsg1-9.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2393 Oct 27 12:07 velvet_1.2.10+dfsg1-9.dsc -rw-r--r-- 1 jenkins jenkins 7674 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8556 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3095 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.changes -rw-r--r-- 1 jenkins jenkins 658092 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 1489 Oct 27 12:07 velvet_1.2.10+dfsg1-9_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2: total 0 Sun Oct 27 12:07:42 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 27 00:03:58 -12 2024 I: pbuilder-time-stamp: 1730030638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [velvet_1.2.10+dfsg1-9.dsc] I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz] I: copying [./velvet_1.2.10+dfsg1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Aug 7 10:20:32 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-9.dsc: no acceptable signature found dpkg-source: info: extracting velvet in velvet-1.2.10+dfsg1 dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2865984/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='09a67f08ce4e49b8b58571bb55c491e4' 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='2865984' 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.p5QOSgFE/pbuilderrc_4fr1 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1 --logfile b1/build.log velvet_1.2.10+dfsg1-9.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2865984/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20056 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended 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-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu72{a} libkpathsea6{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libsm6{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} ucf{a} x11-common{a} xdg-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dvisvgm libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 74.5 MB of archives. After unpacking 244 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-4 [153 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-3 [34.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 60 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b1 [23.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-4 [47.9 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-4 [60.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1 [300 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-4 [106 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-4 [7373 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20240829-2 [22.7 MB] Get: 77 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Fetched 74.5 MB in 0s (216 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 20056 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_arm64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../10-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-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 .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../30-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../31-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../32-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../33-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... 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Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240829-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up texlive-latex-base (2024.20240829-2) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/velvet-1.2.10+dfsg1/ && 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 > ../velvet_1.2.10+dfsg1-9_source.changes dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory rm: cannot remove './velvet*': No such file or directory make[2]: [Makefile:45: clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm -rf zlib rm -rf third-party rm -rf debian.upstream rm -f *.pdf find -name '._*' -delete rm -rf contrib/MetaVelvet* rm -rf contrib/VelvetOptimiser* make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' touch zlib #Make _long version dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_long ; mv velvetg velvetg_long #Make _63 kmer version dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_63 ; mv velvetg velvetg_63 #And also one with both options dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_63_long ; mv velvetg velvetg_63_long #Make _127 kmer version dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_127 ; mv velvetg velvetg_127 #And also one with both options dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_127_long ; mv velvetg velvetg_127_long touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Manual.aux. 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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 331. Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 354. LaTeX Warning: Reference `sec:kmercov' on page 8 undefined on input line 358. LaTeX Warning: Reference `sec:expcov' on page 8 undefined on input line 358. Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [8] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] LaTeX Warning: Reference `sec:hashing' on page 9 undefined on input line 377. LaTeX Warning: Reference `sec:kmercov' on page 9 undefined on input line 379. LaTeX Warning: Reference `sec:pairedformat' on page 9 undefined on input line 3 95. Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [9] [10] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:amos' on page 11 undefined on input line 455. Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 11 undefined on input line 470. Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set LaTeX Warning: Reference `sec:paper' on page 11 undefined on input line 499. [11] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [12] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [13] LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 593. LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 605. Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 615. [14] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 642. Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 683 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 695. LaTeX Warning: Reference `sec:kmercov' on page 16 undefined on input line 695. [16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /build/reproducible-path/velvet-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on Manual.pdf (21 pages, 432098 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./Manual.out ) (./Manual.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] [6] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov [15] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [16] [17] [18 <./Suis_plot_1.pdf>] [19 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [20] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [21] [22] (./Manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Manual.pdf (22 pages, 440025 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 145--145 [] \OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_sequ ences.fa[] [5] (./Columbus_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /build/reproducible-path/velvet-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 88603 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_auto_test -O--no-parallel make -j1 test make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[1]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:49: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] 1060 | RefInfo refElem; | ^~~~~~~ src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from src/passageMarker.c:22: In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:291:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:288:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:298:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:296:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ In file included from /usr/include/stdio.h:970, from src/readSet.c:22: In function 'snprintf', inlined from 'addMapping' at src/readSet.c:753:4, inlined from 'readCigar' at src/readSet.c:799:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 786 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) { | ~~~~~~~^~~~~~ In function 'snprintf', inlined from 'addMapping' at src/readSet.c:751:4, inlined from 'readCigar' at src/readSet.c:799:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 786 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) { | ~~~~~~~^~~~~~ src/readSet.c: In function 'importReadSet': src/readSet.c:1616:25: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 1616 | strncpy(sequence + bpCount, line, lineLength); | ^ src/readSet.c:1615:38: note: length computed here 1615 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:314:33: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] 314 | RefInfo refElem; | ^~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:414:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 414 | if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file)) | ^~ src/preGraphConstruction.c:416:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 416 | seqReadInfo->m_pFile = file; | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ src/kmer.c: At top level: src/kmer.c:31:22: warning: 'charLeftFilter' defined but not used [-Wunused-const-variable=] 31 | static const uint8_t charLeftFilter = (uint8_t) 3 << 6; | ^~~~~~~~~~~~~~ src/kmer.c:30:23: warning: 'intLeftFilter' defined but not used [-Wunused-const-variable=] 30 | static const uint16_t intLeftFilter = (uint16_t) 3 << 14; | ^~~~~~~~~~~~~ src/kmer.c:29:23: warning: 'longLeftFilter' defined but not used [-Wunused-const-variable=] 29 | static const uint32_t longLeftFilter = (uint32_t) 3 << 30; | ^~~~~~~~~~~~~~ src/kmer.c:28:23: warning: 'longLongLeftFilter' defined but not used [-Wunused-const-variable=] 28 | static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; | ^~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'pcloseNoStderr': src/autoOpen.c:49:13: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int rc, status; | ^~ src/autoOpen.c: At top level: src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] 56 | static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL}; | ^~~~~ src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cd tests && ./run-tests.sh [Sun Oct 27 12:06:58 2024] Running Velvet Test Suite [Sun Oct 27 12:06:58 2024] Found ../velveth, ok [Sun Oct 27 12:06:58 2024] Found ../velvetg, ok [Sun Oct 27 12:06:58 2024] Found Sequences.31, ok [Sun Oct 27 12:06:58 2024] Found Roadmaps.31, ok [Sun Oct 27 12:06:58 2024] Found read1.fq.gz, ok [Sun Oct 27 12:06:58 2024] Found read2.fq.gz, ok [Sun Oct 27 12:06:58 2024] Found reads.fq.gz, ok [Sun Oct 27 12:06:58 2024] Found read1.fa.gz, ok [Sun Oct 27 12:06:58 2024] Found read2.fa.gz, ok [Sun Oct 27 12:06:58 2024] Found reads.fa.gz, ok [Sun Oct 27 12:06:58 2024] making test folder: velvet.test.UFjyu8 [Sun Oct 27 12:06:58 2024] running test 1 of 5: fasta_eq_fastq_ascii.t [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] ok [Sun Oct 27 12:07:00 2024] passed test 1 [Sun Oct 27 12:07:00 2024] running test 2 of 5: fasta_eq_fastq_binary.t [Sun Oct 27 12:07:01 2024] ok [Sun Oct 27 12:07:01 2024] ok [Sun Oct 27 12:07:01 2024] passed test 2 [Sun Oct 27 12:07:01 2024] running test 3 of 5: fmt_auto_mode.t [Sun Oct 27 12:07:03 2024] ok [Sun Oct 27 12:07:03 2024] ok [Sun Oct 27 12:07:03 2024] passed test 3 [Sun Oct 27 12:07:03 2024] running test 4 of 5: interleaved_eq_separate.t [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] passed test 4 [Sun Oct 27 12:07:07 2024] running test 5 of 5: mismatched_separates.t [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] ok [Sun Oct 27 12:07:07 2024] passed test 5 [Sun Oct 27 12:07:07 2024] removing test folder: velvet.test.UFjyu8 [Sun Oct 27 12:07:07 2024] passed all 5 tests [Sun Oct 27 12:07:07 2024] hooray! make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel dh_install -O--no-parallel dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_installexamples -i xz -6 debian/velvet-example/usr/share/doc/velvet/examples/* sed -i 's?=\.\./velvet?=/usr/bin/velvet?' debian/velvet-tests/usr/share/doc/velvet/tests/run-tests.functions make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_compress -X.pdf -X.c -X.pl -X.h -X.xz make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-9_all.deb'. dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-9_all.deb'. dpkg-genbuildinfo --build=binary -O../velvet_1.2.10+dfsg1-9_arm64.buildinfo dpkg-genchanges --build=binary -O../velvet_1.2.10+dfsg1-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2865984 and its subdirectories I: Current time: Sun Oct 27 00:07:39 -12 2024 I: pbuilder-time-stamp: 1730030859 Sun Oct 27 12:07:43 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun Oct 27 12:07:43 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun Oct 27 12:07:43 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sun Oct 27 12:07:43 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Uh9Xfi' ==================================================================================== Sat Nov 29 18:30:44 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 velvet unstable /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE 1.2.10+dfsg1-9" as arguments. Sat Nov 29 18:30:44 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-z1hI5ciT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 29 18:30:44 UTC 2025 I: Downloading source for unstable/velvet=1.2.10+dfsg1-9 Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.7 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (dsc) [2393 B] Get:2 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (tar) [13.6 MB] Get:3 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (diff) [18.5 kB] Fetched 13.7 MB in 0s (123 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.7 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (dsc) [2393 B] Get:2 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (tar) [13.6 MB] Get:3 http://deb.debian.org/debian unstable/main velvet 1.2.10+dfsg1-9 (diff) [18.5 kB] Fetched 13.7 MB in 0s (123 MB/s) Download complete and in download only mode ============================================================================= Re-Building velvet in unstable on arm64 on codethink03-arm64 now. Date: Sat Nov 29 18:30:45 GMT 2025 Date UTC: Sat Nov 29 18:30:45 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/pbuilderrc_IuuN + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' velvet = debian-installer -o velvet = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' velvet = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/pbuilderrc_IuuN --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2 --logfile b2/build.log velvet_1.2.10+dfsg1-9.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 30 08:30:45 +14 2025 I: pbuilder-time-stamp: 1764441045 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [velvet_1.2.10+dfsg1-9.dsc] I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz] I: copying [./velvet_1.2.10+dfsg1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Aug 7 10:20:32 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-9.dsc: no acceptable signature found dpkg-source: info: extracting velvet in velvet-1.2.10+dfsg1 dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 29 18:30 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=fe8cd3a84a844e2cabca9a1b275dff80 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3920701 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/pbuilderrc_IuuN --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2 --logfile b2/build.log velvet_1.2.10+dfsg1-9.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20056 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended 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-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu72{a} libkpathsea6{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libsm6{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} ucf{a} x11-common{a} xdg-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dvisvgm libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 74.5 MB of archives. After unpacking 244 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-4 [153 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-3 [34.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 60 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b1 [23.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-4 [47.9 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-4 [60.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1 [300 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-4 [106 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-4 [7373 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20240829-2 [22.7 MB] Get: 77 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Fetched 74.5 MB in 0s (210 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 20056 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_arm64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../10-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-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 .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../30-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../31-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../32-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../33-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../34-libbrotli1_1.1.0-2+b4_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b4) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../35-libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../36-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../37-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../38-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../39-libpixman-1-0_0.42.2-1+b1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.42.2-1+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../40-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../41-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../42-libxcb1_1.17.0-2_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../43-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../44-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../45-libxcb-render0_1.17.0-2_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../46-libxcb-shm0_1.17.0-2_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../47-libxext6_2%3a1.3.4-1+b2_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../48-libxrender1_1%3a0.9.10-1.1+b1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../49-libcairo2_1.18.2-2_arm64.deb ... Unpacking libcairo2:arm64 (1.18.2-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../50-libglib2.0-0t64_2.82.2-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.2-2) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../51-libgraphite2-3_1.3.14-2_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../52-libharfbuzz0b_10.0.1-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../53-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../54-libice6_2%3a1.0.10-1+b1_arm64.deb ... Unpacking libice6:arm64 (2:1.0.10-1+b1) ... Selecting previously unselected package libkpathsea6:arm64. Preparing to unpack .../55-libkpathsea6_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libmpfi0:arm64. Preparing to unpack .../56-libmpfi0_1.5.4+ds-3_arm64.deb ... Unpacking libmpfi0:arm64 (1.5.4+ds-3) ... Selecting previously unselected package libpaper1:arm64. Preparing to unpack .../57-libpaper1_1.1.29+b1_arm64.deb ... Unpacking libpaper1:arm64 (1.1.29+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../58-libpaper-utils_1.1.29+b1_arm64.deb ... Unpacking libpaper-utils (1.1.29+b1) ... Selecting previously unselected package libpotrace0:arm64. Preparing to unpack .../59-libpotrace0_1.16-2+b1_arm64.deb ... Unpacking libpotrace0:arm64 (1.16-2+b1) ... Selecting previously unselected package libptexenc1:arm64. Preparing to unpack .../60-libptexenc1_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../61-libsm6_2%3a1.2.3-1+b1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.3-1+b1) ... Selecting previously unselected package libsynctex2:arm64. Preparing to unpack .../62-libsynctex2_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libteckit0:arm64. Preparing to unpack .../63-libteckit0_2.5.12+ds1-1_arm64.deb ... Unpacking libteckit0:arm64 (2.5.12+ds1-1) ... Selecting previously unselected package libtexlua53-5:arm64. Preparing to unpack .../64-libtexlua53-5_2024.20240313.70630+ds-4_arm64.deb ... Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-4) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../65-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../66-libxmu6_2%3a1.1.3-3+b2_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.3-3+b2) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../67-libxpm4_1%3a3.5.17-1+b1_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.17-1+b1) ... Selecting previously unselected package libxaw7:arm64. Preparing to unpack .../68-libxaw7_2%3a1.0.14-1+b2_arm64.deb ... Unpacking libxaw7:arm64 (2:1.0.14-1+b2) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../69-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libzzip-0-13t64:arm64. Preparing to unpack .../70-libzzip-0-13t64_0.13.72+dfsg.1-1.3_arm64.deb ... Unpacking libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Selecting previously unselected package t1utils. Preparing to unpack .../71-t1utils_1.41-4_arm64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package tex-common. Preparing to unpack .../72-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../73-texlive-binaries_2024.20240313.70630+ds-4_arm64.deb ... Unpacking texlive-binaries (2024.20240313.70630+ds-4) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../74-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package texlive-base. Preparing to unpack .../75-texlive-base_2024.20240829-2_all.deb ... Unpacking texlive-base (2024.20240829-2) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../76-texlive-latex-base_2024.20240829-2_all.deb ... Unpacking texlive-latex-base (2024.20240829-2) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../77-texlive-latex-recommended_2024.20240829-2_all.deb ... Unpacking texlive-latex-recommended (2024.20240829-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../78-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:arm64 (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:arm64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:arm64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-4) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-4) ... Setting up libpotrace0:arm64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up gettext (0.22.5-2) ... Setting up libxpm4:arm64 (1:3.5.17-1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:arm64 (2024.20240313.70630+ds-4) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up libpaper1:arm64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libxmu6:arm64 (2:1.1.3-3+b2) ... Setting up debhelper (13.20) ... Setting up libxaw7:arm64 (2:1.0.14-1+b2) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240829-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up texlive-latex-base (2024.20240829-2) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/velvet-1.2.10+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../velvet_1.2.10+dfsg1-9_source.changes dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory rm: cannot remove './velvet*': No such file or directory make[2]: [Makefile:45: clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm -rf zlib rm -rf third-party rm -rf debian.upstream rm -f *.pdf find -name '._*' -delete rm -rf contrib/MetaVelvet* rm -rf contrib/VelvetOptimiser* make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' touch zlib #Make _long version dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_long ; mv velvetg velvetg_long #Make _63 kmer version dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_63 ; mv velvetg velvetg_63 #And also one with both options dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_63_long ; mv velvetg velvetg_63_long #Make _127 kmer version dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_127 ; mv velvetg velvetg_127 #And also one with both options dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' mv velveth velveth_127_long ; mv velvetg velvetg_127_long touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Manual.aux. 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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 331. Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 354. 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[16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /build/reproducible-path/velvet-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on Manual.pdf (21 pages, 432098 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./Manual.out ) (./Manual.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] [6] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov [15] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [16] [17] [18 <./Suis_plot_1.pdf>] [19 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [20] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [21] [22] (./Manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Manual.pdf (22 pages, 440025 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 145--145 [] \OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_sequ ences.fa[] [5] (./Columbus_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /build/reproducible-path/velvet-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 88603 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp -O3 -Wl,-z,relro -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_auto_test -O--no-parallel make -j1 test make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[1]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:49: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] 1060 | RefInfo refElem; | ^~~~~~~ src/splayTable.c: In function 'scanReferenceSequences': src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'scanBinaryReferenceSequences': src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from src/passageMarker.c:22: In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:291:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:288:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:298:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'readPassageMarker' at src/passageMarker.c:296:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ In file included from /usr/include/stdio.h:970, from src/readSet.c:22: In function 'snprintf', inlined from 'addMapping' at src/readSet.c:753:4, inlined from 'readCigar' at src/readSet.c:799:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 786 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) { | ~~~~~~~^~~~~~ In function 'snprintf', inlined from 'addMapping' at src/readSet.c:751:4, inlined from 'readCigar' at src/readSet.c:799:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 786 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) { | ~~~~~~~^~~~~~ src/readSet.c: In function 'importReadSet': src/readSet.c:1616:25: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 1616 | strncpy(sequence + bpCount, line, lineLength); | ^ src/readSet.c:1615:38: note: length computed here 1615 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:314:33: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] 314 | RefInfo refElem; | ^~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function 'addPreArcToPreNode_pg': src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function 'removePreArcFromList_pg': src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:414:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 414 | if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file)) | ^~ src/preGraphConstruction.c:416:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 416 | seqReadInfo->m_pFile = file; | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function 'pushNucleotide': src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ src/kmer.c: At top level: src/kmer.c:31:22: warning: 'charLeftFilter' defined but not used [-Wunused-const-variable=] 31 | static const uint8_t charLeftFilter = (uint8_t) 3 << 6; | ^~~~~~~~~~~~~~ src/kmer.c:30:23: warning: 'intLeftFilter' defined but not used [-Wunused-const-variable=] 30 | static const uint16_t intLeftFilter = (uint16_t) 3 << 14; | ^~~~~~~~~~~~~ src/kmer.c:29:23: warning: 'longLeftFilter' defined but not used [-Wunused-const-variable=] 29 | static const uint32_t longLeftFilter = (uint32_t) 3 << 30; | ^~~~~~~~~~~~~~ src/kmer.c:28:23: warning: 'longLongLeftFilter' defined but not used [-Wunused-const-variable=] 28 | static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; | ^~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'pcloseNoStderr': src/autoOpen.c:49:13: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int rc, status; | ^~ src/autoOpen.c: At top level: src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] 56 | static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL}; | ^~~~~ src/autoOpen.c: In function 'popenNoStderr': src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cd tests && ./run-tests.sh [Sat Nov 29 18:33:58 2025] Running Velvet Test Suite [Sat Nov 29 18:33:58 2025] Found ../velveth, ok [Sat Nov 29 18:33:58 2025] Found ../velvetg, ok [Sat Nov 29 18:33:58 2025] Found Sequences.31, ok [Sat Nov 29 18:33:58 2025] Found Roadmaps.31, ok [Sat Nov 29 18:33:58 2025] Found read1.fq.gz, ok [Sat Nov 29 18:33:58 2025] Found read2.fq.gz, ok [Sat Nov 29 18:33:58 2025] Found reads.fq.gz, ok [Sat Nov 29 18:33:58 2025] Found read1.fa.gz, ok [Sat Nov 29 18:33:58 2025] Found read2.fa.gz, ok [Sat Nov 29 18:33:58 2025] Found reads.fa.gz, ok [Sat Nov 29 18:33:58 2025] making test folder: velvet.test.SDU4GB [Sat Nov 29 18:33:58 2025] running test 1 of 5: fasta_eq_fastq_ascii.t [Sat Nov 29 18:34:00 2025] ok [Sat Nov 29 18:34:00 2025] ok [Sat Nov 29 18:34:00 2025] ok [Sat Nov 29 18:34:00 2025] ok [Sat Nov 29 18:34:00 2025] passed test 1 [Sat Nov 29 18:34:00 2025] running test 2 of 5: fasta_eq_fastq_binary.t [Sat Nov 29 18:34:01 2025] ok [Sat Nov 29 18:34:01 2025] ok [Sat Nov 29 18:34:01 2025] passed test 2 [Sat Nov 29 18:34:01 2025] running test 3 of 5: fmt_auto_mode.t [Sat Nov 29 18:34:03 2025] ok [Sat Nov 29 18:34:03 2025] ok [Sat Nov 29 18:34:03 2025] passed test 3 [Sat Nov 29 18:34:03 2025] running test 4 of 5: interleaved_eq_separate.t [Sat Nov 29 18:34:07 2025] ok [Sat Nov 29 18:34:07 2025] ok [Sat Nov 29 18:34:07 2025] passed test 4 [Sat Nov 29 18:34:07 2025] running test 5 of 5: mismatched_separates.t [Sat Nov 29 18:34:07 2025] ok [Sat Nov 29 18:34:07 2025] ok [Sat Nov 29 18:34:07 2025] passed test 5 [Sat Nov 29 18:34:07 2025] removing test folder: velvet.test.SDU4GB [Sat Nov 29 18:34:07 2025] passed all 5 tests [Sat Nov 29 18:34:07 2025] hooray! make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel dh_install -O--no-parallel dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_installexamples -i xz -6 debian/velvet-example/usr/share/doc/velvet/examples/* sed -i 's?=\.\./velvet?=/usr/bin/velvet?' debian/velvet-tests/usr/share/doc/velvet/tests/run-tests.functions make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_compress -X.pdf -X.c -X.pl -X.h -X.xz make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-9_arm64.deb'. dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-9_all.deb'. dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-9_all.deb'. dpkg-genbuildinfo --build=binary -O../velvet_1.2.10+dfsg1-9_arm64.buildinfo dpkg-genchanges --build=binary -O../velvet_1.2.10+dfsg1-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3920701 and its subdirectories I: Current time: Sun Nov 30 08:34:40 +14 2025 I: pbuilder-time-stamp: 1764441280 + false + set +x Sat Nov 29 18:34:40 UTC 2025 I: Signing ./b2/velvet_1.2.10+dfsg1-9_arm64.buildinfo as velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc Sat Nov 29 18:34:40 UTC 2025 I: Signed ./b2/velvet_1.2.10+dfsg1-9_arm64.buildinfo as ./b2/velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc Sat Nov 29 18:34:40 UTC 2025 - build #2 for velvet/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Sat Nov 29 18:34:40 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-z1hI5ciT, removing. /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE: total 340 drwxr-xr-x 2 jenkins jenkins 4096 Oct 27 12:07 b1 drwxr-xr-x 2 jenkins jenkins 4096 Oct 27 12:11 b2 -rw------- 1 jenkins jenkins 328619 Oct 27 12:07 rbuildlog.o4wvCsB -rw-r--r-- 1 jenkins jenkins 2393 Aug 7 10:31 velvet_1.2.10+dfsg1-9.dsc /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1: total 18056 -rw-r--r-- 1 jenkins jenkins 324786 Oct 27 12:07 build.log -rw-r--r-- 1 jenkins jenkins 990736 Oct 27 12:07 velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 3381368 Oct 27 12:07 velvet-example_1.2.10+dfsg1-9_all.deb -rw-r--r-- 1 jenkins jenkins 2078100 Oct 27 12:07 velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 198824 Oct 27 12:07 velvet-long_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 10748728 Oct 27 12:07 velvet-tests_1.2.10+dfsg1-9_all.deb -rw-r--r-- 1 jenkins jenkins 18476 Oct 27 12:07 velvet_1.2.10+dfsg1-9.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2393 Oct 27 12:07 velvet_1.2.10+dfsg1-9.dsc -rw-r--r-- 1 jenkins jenkins 7674 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8556 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3095 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.changes -rw-r--r-- 1 jenkins jenkins 658092 Oct 27 12:07 velvet_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 1489 Oct 27 12:07 velvet_1.2.10+dfsg1-9_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2: total 18056 -rw-r--r-- 1 jenkins jenkins 326731 Oct 27 12:11 build.log -rw-r--r-- 1 jenkins jenkins 990736 Oct 27 12:11 velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 3381368 Oct 27 12:11 velvet-example_1.2.10+dfsg1-9_all.deb -rw-r--r-- 1 jenkins jenkins 2078100 Oct 27 12:11 velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 198824 Oct 27 12:11 velvet-long_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 10748728 Oct 27 12:11 velvet-tests_1.2.10+dfsg1-9_all.deb -rw-r--r-- 1 jenkins jenkins 18476 Oct 27 12:11 velvet_1.2.10+dfsg1-9.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2393 Oct 27 12:11 velvet_1.2.10+dfsg1-9.dsc -rw-r--r-- 1 jenkins jenkins 7674 Oct 27 12:11 velvet_1.2.10+dfsg1-9_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8556 Oct 27 12:11 velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3095 Oct 27 12:11 velvet_1.2.10+dfsg1-9_arm64.changes -rw-r--r-- 1 jenkins jenkins 658092 Oct 27 12:11 velvet_1.2.10+dfsg1-9_arm64.deb -rw-r--r-- 1 jenkins jenkins 1489 Oct 27 12:11 velvet_1.2.10+dfsg1-9_source.changes Sun Oct 27 12:11:45 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun Oct 27 12:11:46 UTC 2024 I: velvet_1.2.10+dfsg1-9_arm64.changes: Format: 1.8 Date: Wed, 07 Aug 2024 11:51:33 +0200 Source: velvet Binary: velvet velvet-dbgsym velvet-example velvet-long velvet-long-dbgsym velvet-tests Architecture: arm64 all Version: 1.2.10+dfsg1-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler velvet-long - Nucleic acid sequence assembler for very short reads, long versio velvet-tests - Test data for the Velvet sequence assembler Closes: 1075617 Changes: velvet (1.2.10+dfsg1-9) unstable; urgency=medium . * Team upload. * gcc-14.patch: new: fix incompatible pointer types. (Closes: #1075617) * d/control: declare compliance to standards version 4.7.0. * hardening.patch: also propagate CPPFLAGS. This allows fortifying the source where applicable. Checksums-Sha1: 0226aa93aeae169aca9e1fbfca2b6a9593981228 990736 velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb a02603751523d1b4bc4f3e11d8aa81b1b145b2d6 3381368 velvet-example_1.2.10+dfsg1-9_all.deb fe4994298f9033cb299dd6b01ccdf0959f5ae1d4 2078100 velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb 0adb508d31db1bc4f50ce9848934d032c25bb7dd 198824 velvet-long_1.2.10+dfsg1-9_arm64.deb 4eff0b868f770113371a378891e5e3aa02ce8cb0 10748728 velvet-tests_1.2.10+dfsg1-9_all.deb 38f16df10f8f1df0c471fc805a8070c2477159ae 7674 velvet_1.2.10+dfsg1-9_arm64.buildinfo 1029e306e3439f9c3239e3d2d4fbf973ae3241fa 658092 velvet_1.2.10+dfsg1-9_arm64.deb Checksums-Sha256: fd58d56abc5e69b1d064e10542365b8b9a101aa7e802f3c9486f57a219a686f9 990736 velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb d8b4ca240d4a260d64555b2a93eb2cc3cb5ebd74f0e797321de8daaf0d57e51b 3381368 velvet-example_1.2.10+dfsg1-9_all.deb a1b9b983c6695204ad026849a68510df5e059bb9c4753b74ec914f823ddf7b0e 2078100 velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb 2392f385ca63ced574e1ccaf30f634e10acab69ea15deddd07522b405490e740 198824 velvet-long_1.2.10+dfsg1-9_arm64.deb 137cbf93af56e00696a71c75d509afa2fa2dd7c54f06f1c5a08a69a44f304172 10748728 velvet-tests_1.2.10+dfsg1-9_all.deb 6edb5411dcea044ecc9f2d27ef169ebd8a038247e7260befcbad3a98620e531f 7674 velvet_1.2.10+dfsg1-9_arm64.buildinfo 4f85e71bf40c080fee181af21d1a6d3ec685785ecb921a2f8b3937b441907871 658092 velvet_1.2.10+dfsg1-9_arm64.deb Files: 73323c576d558fedf86d7a7441ea1b4f 990736 debug optional velvet-dbgsym_1.2.10+dfsg1-9_arm64.deb 8bf56be216b8febdeddfa8a2167da265 3381368 science optional velvet-example_1.2.10+dfsg1-9_all.deb 3484672bbfd464fe379f0b5a684cb075 2078100 debug optional velvet-long-dbgsym_1.2.10+dfsg1-9_arm64.deb 5c45500e0ae04f7a1688f2b65532d0c4 198824 science optional velvet-long_1.2.10+dfsg1-9_arm64.deb 0011fc033ac196bea82677b6c5006ae1 10748728 science optional velvet-tests_1.2.10+dfsg1-9_all.deb 7ef9f326a5a6389e5e494366f41b747c 7674 science optional velvet_1.2.10+dfsg1-9_arm64.buildinfo 901fc49bda393a1df277b05b78ba8f17 658092 science optional velvet_1.2.10+dfsg1-9_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/velvet_1.2.10+dfsg1-9.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/velvet_1.2.10+dfsg1-9.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/velvet_1.2.10+dfsg1-9.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/velvet_1.2.10+dfsg1-9.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/velvet_1.2.10+dfsg1-9_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/velvet_1.2.10+dfsg1-9.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-10-27 12:07:41.022199106 +0000 +++ b2/build.log 2024-10-27 12:11:42.237641306 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 27 00:03:58 -12 2024 -I: pbuilder-time-stamp: 1730030638 +I: Current time: Sun Nov 30 08:30:45 +14 2025 +I: pbuilder-time-stamp: 1764441045 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2865984/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 29 18:30 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='09a67f08ce4e49b8b58571bb55c491e4' - 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='2865984' - PS1='# ' - PS2='> ' + INVOCATION_ID=fe8cd3a84a844e2cabca9a1b275dff80 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3920701 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.p5QOSgFE/pbuilderrc_4fr1 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1 --logfile b1/build.log velvet_1.2.10+dfsg1-9.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/pbuilderrc_IuuN --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2 --logfile b2/build.log velvet_1.2.10+dfsg1-9.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2865984/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -201,7 +233,7 @@ Get: 77 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] -Fetched 74.5 MB in 0s (216 MB/s) +Fetched 74.5 MB in 0s (210 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 20056 files and directories currently installed.) @@ -551,7 +583,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/velvet-1.2.10+dfsg1/ && 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 > ../velvet_1.2.10+dfsg1-9_source.changes +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/velvet-1.2.10+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../velvet_1.2.10+dfsg1-9_source.changes dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-9 dpkg-buildpackage: info: source distribution unstable @@ -3523,43 +3559,43 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cd tests && ./run-tests.sh -[Sun Oct 27 12:06:58 2024] Running Velvet Test Suite -[Sun Oct 27 12:06:58 2024] Found ../velveth, ok -[Sun Oct 27 12:06:58 2024] Found ../velvetg, ok -[Sun Oct 27 12:06:58 2024] Found Sequences.31, ok -[Sun Oct 27 12:06:58 2024] Found Roadmaps.31, ok -[Sun Oct 27 12:06:58 2024] Found read1.fq.gz, ok -[Sun Oct 27 12:06:58 2024] Found read2.fq.gz, ok -[Sun Oct 27 12:06:58 2024] Found reads.fq.gz, ok -[Sun Oct 27 12:06:58 2024] Found read1.fa.gz, ok -[Sun Oct 27 12:06:58 2024] Found read2.fa.gz, ok -[Sun Oct 27 12:06:58 2024] Found reads.fa.gz, ok -[Sun Oct 27 12:06:58 2024] making test folder: velvet.test.UFjyu8 -[Sun Oct 27 12:06:58 2024] running test 1 of 5: fasta_eq_fastq_ascii.t -[Sun Oct 27 12:07:00 2024] ok -[Sun Oct 27 12:07:00 2024] ok -[Sun Oct 27 12:07:00 2024] ok -[Sun Oct 27 12:07:00 2024] ok -[Sun Oct 27 12:07:00 2024] passed test 1 -[Sun Oct 27 12:07:00 2024] running test 2 of 5: fasta_eq_fastq_binary.t -[Sun Oct 27 12:07:01 2024] ok -[Sun Oct 27 12:07:01 2024] ok -[Sun Oct 27 12:07:01 2024] passed test 2 -[Sun Oct 27 12:07:01 2024] running test 3 of 5: fmt_auto_mode.t -[Sun Oct 27 12:07:03 2024] ok -[Sun Oct 27 12:07:03 2024] ok -[Sun Oct 27 12:07:03 2024] passed test 3 -[Sun Oct 27 12:07:03 2024] running test 4 of 5: interleaved_eq_separate.t -[Sun Oct 27 12:07:07 2024] ok -[Sun Oct 27 12:07:07 2024] ok -[Sun Oct 27 12:07:07 2024] passed test 4 -[Sun Oct 27 12:07:07 2024] running test 5 of 5: mismatched_separates.t -[Sun Oct 27 12:07:07 2024] ok -[Sun Oct 27 12:07:07 2024] ok -[Sun Oct 27 12:07:07 2024] passed test 5 -[Sun Oct 27 12:07:07 2024] removing test folder: velvet.test.UFjyu8 -[Sun Oct 27 12:07:07 2024] passed all 5 tests -[Sun Oct 27 12:07:07 2024] hooray! +[Sat Nov 29 18:33:58 2025] Running Velvet Test Suite +[Sat Nov 29 18:33:58 2025] Found ../velveth, ok +[Sat Nov 29 18:33:58 2025] Found ../velvetg, ok +[Sat Nov 29 18:33:58 2025] Found Sequences.31, ok +[Sat Nov 29 18:33:58 2025] Found Roadmaps.31, ok +[Sat Nov 29 18:33:58 2025] Found read1.fq.gz, ok +[Sat Nov 29 18:33:58 2025] Found read2.fq.gz, ok +[Sat Nov 29 18:33:58 2025] Found reads.fq.gz, ok +[Sat Nov 29 18:33:58 2025] Found read1.fa.gz, ok +[Sat Nov 29 18:33:58 2025] Found read2.fa.gz, ok +[Sat Nov 29 18:33:58 2025] Found reads.fa.gz, ok +[Sat Nov 29 18:33:58 2025] making test folder: velvet.test.SDU4GB +[Sat Nov 29 18:33:58 2025] running test 1 of 5: fasta_eq_fastq_ascii.t +[Sat Nov 29 18:34:00 2025] ok +[Sat Nov 29 18:34:00 2025] ok +[Sat Nov 29 18:34:00 2025] ok +[Sat Nov 29 18:34:00 2025] ok +[Sat Nov 29 18:34:00 2025] passed test 1 +[Sat Nov 29 18:34:00 2025] running test 2 of 5: fasta_eq_fastq_binary.t +[Sat Nov 29 18:34:01 2025] ok +[Sat Nov 29 18:34:01 2025] ok +[Sat Nov 29 18:34:01 2025] passed test 2 +[Sat Nov 29 18:34:01 2025] running test 3 of 5: fmt_auto_mode.t +[Sat Nov 29 18:34:03 2025] ok +[Sat Nov 29 18:34:03 2025] ok +[Sat Nov 29 18:34:03 2025] passed test 3 +[Sat Nov 29 18:34:03 2025] running test 4 of 5: interleaved_eq_separate.t +[Sat Nov 29 18:34:07 2025] ok +[Sat Nov 29 18:34:07 2025] ok +[Sat Nov 29 18:34:07 2025] passed test 4 +[Sat Nov 29 18:34:07 2025] running test 5 of 5: mismatched_separates.t +[Sat Nov 29 18:34:07 2025] ok +[Sat Nov 29 18:34:07 2025] ok +[Sat Nov 29 18:34:07 2025] passed test 5 +[Sat Nov 29 18:34:07 2025] removing test folder: velvet.test.SDU4GB +[Sat Nov 29 18:34:07 2025] passed all 5 tests +[Sat Nov 29 18:34:07 2025] hooray! make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel @@ -3614,12 +3650,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3920701/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2865984 and its subdirectories -I: Current time: Sun Oct 27 00:07:39 -12 2024 -I: pbuilder-time-stamp: 1730030859 +I: removing directory /srv/workspace/pbuilder/3920701 and its subdirectories +I: Current time: Sun Nov 30 08:34:40 +14 2025 +I: pbuilder-time-stamp: 1764441280 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/velvet_1.2.10+dfsg1-9.diff: 71.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/velvet_1.2.10+dfsg1-9.diff.gz b2/build.log: 93.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 93.5% -- replaced with stdout Sun Oct 27 12:11:47 UTC 2024 I: diffoscope 282 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_velvet_unstable_arm64_1730031107 + touch /var/log/reproducible-builds/diffoscope_stamp_velvet_unstable_arm64_1730031107 + RESULT=0 + systemd-run '--description=diffoscope on velvet/1.2.10+dfsg1-9 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_7-41826 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE --run-session -c jenkins-reproducible-unstable-diffoscope-88174b8d-857d-43a2-acc0-9e6f099b66ee -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/dbd-tmp-vXPfdZo ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/velvet_1.2.10+dfsg1-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/velvet_1.2.10+dfsg1-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/velvet_1.2.10+dfsg1-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1/velvet_1.2.10+dfsg1-9_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2/velvet_1.2.10+dfsg1-9_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_7-41826.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/velvet_1.2.10+dfsg1-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/velvet_1.2.10+dfsg1-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/velvet_1.2.10+dfsg1-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b1/velvet_1.2.10+dfsg1-9_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.p5QOSgFE/b2/velvet_1.2.10+dfsg1-9_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.582s) 0.582s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.210s) 0.210s 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: 936ms CPU time consumed: 936ms _ _ __ _____| |_ _____| |_ \ \ / / _ \ \ \ / / _ \ __| \ V / __/ |\ V / __/ |_ \_/ \___|_| \_/ \___|\__| Sun Oct 27 12:11:48 UTC 2024 I: diffoscope 282 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 27 12:11:48 UTC 2024 I: velvet from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-10-27 12:11:49] INFO: Starting at 2024-10-27 12:11:49.348621 [2024-10-27 12:11:49] INFO: Generating the pages of 1 package(s) [2024-10-27 12:11:49] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/velvet didn't produce a buildlog, even though it has been built. [2024-10-27 12:11:50] INFO: Finished at 2024-10-27 12:11:50.034095, took: 0:00:00.685479 Sun Oct 27 12:11:50 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/velvet.html Sun Oct 27 12:11:50 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Oct 27 12:11:50 UTC 2024 I: Submitting 12K b1/velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc https://buildinfo.debian.net/38f16df10f8f1df0c471fc805a8070c2477159ae/velvet_1.2.10+dfsg1-9_all Sun Oct 27 12:11:51 UTC 2024 I: Submitting 12K b2/velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc https://buildinfo.debian.net/7a68007ea2e7d64c0af194181320e93dd47df96c/velvet_1.2.10+dfsg1-9_all Sun Oct 27 12:11:51 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Oct 27 12:11:51 UTC 2024 I: Done submitting .buildinfo files. Sun Oct 27 12:11:51 UTC 2024 I: Removing signed velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc files: removed './b1/velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc' removed './b2/velvet_1.2.10+dfsg1-9_arm64.buildinfo.asc' 1730031111 arm64 unstable velvet Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/velvet_1.2.10+dfsg1-9.rbuild.log: 92.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/velvet_1.2.10+dfsg1-9.rbuild.log.gz [2024-10-27 12:11:52] INFO: Starting at 2024-10-27 12:11:52.317045 [2024-10-27 12:11:52] INFO: Generating the pages of 1 package(s) [2024-10-27 12:11:52] INFO: Finished at 2024-10-27 12:11:52.861110, took: 0:00:00.544074 All cleanup done. Sun Oct 27 12:11:52 UTC 2024 - total duration: 0h 8m 16s. Sun Oct 27 12:11:52 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-LG2eRXz7, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 8min 20.465s CPU time consumed: 9.838s