Mon May 6 17:24:52 UTC 2024 I: starting to build velvet/trixie/amd64 on jenkins on '2024-05-06 17:24' Mon May 6 17:24:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/11006/console.log Mon May 6 17:24:52 UTC 2024 I: Downloading source for trixie/velvet=1.2.10+dfsg1-8 --2024-05-06 17:24:52-- http://deb.debian.org/debian/pool/main/v/velvet/velvet_1.2.10%2bdfsg1-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2270 (2.2K) [text/prs.lines.tag] Saving to: ‘velvet_1.2.10+dfsg1-8.dsc’ 0K .. 100% 334M=0s 2024-05-06 17:24:52 (334 MB/s) - ‘velvet_1.2.10+dfsg1-8.dsc’ saved [2270/2270] Mon May 6 17:24:52 UTC 2024 I: velvet_1.2.10+dfsg1-8.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+dfsg1-8 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/dzerbino/velvet Standards-Version: 4.6.1 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 d038bf3d2c9473b711b6582867fb3c0e7d43b360 17152 velvet_1.2.10+dfsg1-8.debian.tar.xz Checksums-Sha256: 368d760ad56ffa010a2ae72b25d46680ecb7ad8cc573cf6c389848c87b32ee26 13630488 velvet_1.2.10+dfsg1.orig.tar.xz dac824d414948cd356c22459f0f66180e6be86209346da4e67b72227d68bd871 17152 velvet_1.2.10+dfsg1-8.debian.tar.xz Files: 7a58a6d75cdc8b89d1c605033050bbcf 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 867f3efcbd489623ce46364ef2a3ad2f 17152 velvet_1.2.10+dfsg1-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOGXSMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHK9g/9HYJ/3hQ5uVdIpwOZuU1i2Pktq9Aptny4 4HJuNPJ7hf1+oS4/oJ6pT60AXHwBaQIYhf4AtQdD7tuLHXe76KXPCso50k9Umrou T5c9SRgOkzKjq70qYrIxZYorzRf2UH5nBj5fYeg4czcXplkqknUsnf0Ukqn6vp/g zjPKsCDnWvRbfmThvayZjTgykVuNlxvjRWqUUI0CCNNUnsZIo9+STjeCIqLc81Uy CfCEcdu6aROhqqpLCtvbF32We2wETYVFnS73WRmvNtJQ7iInKr/9y9TavSoixZ5J zoZT9vD4lloOZ4daYVrjKlkf+MgdmZYyFE8pSgrnikVwbsShbL3SC8YBe4E1BDEH uFwnCaWEbRquRBdVnWHZFsK78uQq6t8W5zpRBz2ItwEPWgzB5JncJMYVJE/rO2h3 U4L7/ajQTzqckJ6kpCHVpDVBsQMssyOKgFKXNhbF05Ozcf6zTtadmFpK1nJM2ZL1 4pqjPkz1OL2SmhrIW9+1LCowAdGWO0WDKW4AxenR1YurqcEHt/iw6TnOttX5ya2g Fsr8brI+cJRjZO5fLO5oFtdsSl1W/xWY8JV0dBTilfm+fNHyWQ0Ej4pBu1HLXTFh jOVkS6OdpnNq0aDgEoPefkJ6eZuPeko53a8DHg7KlzNEHkAQ7AFDkkE+HPOPIwD8 XR+1Mbs64zY= =Vpgu -----END PGP SIGNATURE----- Mon May 6 17:24:52 UTC 2024 I: Checking whether the package is not for us Mon May 6 17:24:52 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Mon May 6 17:24:52 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Mon May 6 17:28:58 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 6 05:24:54 -12 2024 I: pbuilder-time-stamp: 1715016294 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [velvet_1.2.10+dfsg1-8.dsc] I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz] I: copying [./velvet_1.2.10+dfsg1-8.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 29 19:27:31 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-8.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+dfsg1-8.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/544435/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='df995ee6f63d41bd892c7a540c7e861e' 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='544435' 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.tOESGjXd/pbuilderrc_22Gk --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tOESGjXd/b1 --logfile b1/build.log velvet_1.2.10+dfsg1-8.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' I: uname -a Linux infom01-amd64 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/544435/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19698 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} libbsd0{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} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libsm6{a} libsub-override-perl{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, 80 newly installed, 0 to remove and 0 not upgraded. Need to get 76.8 MB of archives. After unpacking 235 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2023.20230311.66589-9+b2 [154 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2023.20230311.66589-9+b2 [47.2 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2023.20230311.66589-9+b2 [62.2 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2023.20230311.66589-9+b2 [113 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2023.20230311.66589-9+b2 [8495 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 78 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 76.8 MB in 1s (115 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 ... 19698 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... 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Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2023.20230311.66589-9+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:amd64 (2023.20230311.66589-9+b2) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... 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:amd64 (2023.20230311.66589-9+b2) ... Setting up libpotrace0:amd64 (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 (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:amd64 (2023.20230311.66589-9+b2) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up debhelper (13.15.3) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up texlive-binaries (2023.20230311.66589-9+b2) ... 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 (2023.20240207-1) ... 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 (2023.20240207-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Processing triggers for libc-bin (2.38-7) ... 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+dfsg1-8_source.changes dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 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/auxhook/auxhook.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/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. 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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. 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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 2023/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/.texlive2023/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, 432091 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 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/auxhook/auxhook.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/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, 440017 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 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 2023/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/.texlive2023/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, 88596 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 -fcf-protection" 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 -fcf-protection" 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/passageMarker.c: In function 'readPassageMarker': src/passageMarker.c:291:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict] 291 | sprintf(s, "%s %ld -> %ld", s, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 | (long) getNodeID(getNode(getPreviousInSequence(marker))), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | (long) getNodeID(getNode(marker))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/passageMarker.c:288:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict] 288 | sprintf(s, "%s START -> %ld", s, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | (long) getNodeID(getNode(marker))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/passageMarker.c:298:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict] 298 | sprintf(s, "%s -> %ld ", s, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 | (long) getNodeID(getNode(getNextInSequence(marker)))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/passageMarker.c:296:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict] 296 | sprintf(s, "%s -> FINISH", s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ In function 'addMapping', inlined from 'readCigar' at src/readSet.c:796:6: src/readSet.c:750:25: warning: 'snprintf' argument 4 overlaps destination object 'buffer' [-Wrestrict] 750 | snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) - orientation * refCoord->referenceID, (long long) (refCoord->finish - pos - strlen(seq))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:783:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 783 | 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 'addMapping', inlined from 'readCigar' at src/readSet.c:796:6: src/readSet.c:748:25: warning: 'snprintf' argument 4 overlaps destination object 'buffer' [-Wrestrict] 748 | snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) orientation * refCoord->referenceID, (long long) (pos - refCoord->start)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c: In function 'readCigar': src/readSet.c:783:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 783 | 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:1613:25: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 1613 | strncpy(sequence + bpCount, line, lineLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:38: note: length computed here 1612 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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}; | ^~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [Mon May 06 17:28:13 2024] Running Velvet Test Suite [Mon May 06 17:28:13 2024] Found ../velveth, ok [Mon May 06 17:28:13 2024] Found ../velvetg, ok [Mon May 06 17:28:13 2024] Found Sequences.31, ok [Mon May 06 17:28:13 2024] Found Roadmaps.31, ok [Mon May 06 17:28:13 2024] Found read1.fq.gz, ok [Mon May 06 17:28:13 2024] Found read2.fq.gz, ok [Mon May 06 17:28:13 2024] Found reads.fq.gz, ok [Mon May 06 17:28:13 2024] Found read1.fa.gz, ok [Mon May 06 17:28:13 2024] Found read2.fa.gz, ok [Mon May 06 17:28:13 2024] Found reads.fa.gz, ok [Mon May 06 17:28:13 2024] making test folder: velvet.test.IyZKQH [Mon May 06 17:28:13 2024] running test 1 of 5: fasta_eq_fastq_ascii.t [Mon May 06 17:28:15 2024] ok [Mon May 06 17:28:15 2024] ok [Mon May 06 17:28:15 2024] ok [Mon May 06 17:28:15 2024] ok [Mon May 06 17:28:15 2024] passed test 1 [Mon May 06 17:28:15 2024] running test 2 of 5: fasta_eq_fastq_binary.t [Mon May 06 17:28:17 2024] ok [Mon May 06 17:28:17 2024] ok [Mon May 06 17:28:17 2024] passed test 2 [Mon May 06 17:28:17 2024] running test 3 of 5: fmt_auto_mode.t [Mon May 06 17:28:19 2024] ok [Mon May 06 17:28:19 2024] ok [Mon May 06 17:28:19 2024] passed test 3 [Mon May 06 17:28:19 2024] running test 4 of 5: interleaved_eq_separate.t [Mon May 06 17:28:22 2024] ok [Mon May 06 17:28:22 2024] ok [Mon May 06 17:28:22 2024] passed test 4 [Mon May 06 17:28:22 2024] running test 5 of 5: mismatched_separates.t [Mon May 06 17:28:22 2024] ok [Mon May 06 17:28:22 2024] ok [Mon May 06 17:28:22 2024] passed test 5 [Mon May 06 17:28:22 2024] removing test folder: velvet.test.IyZKQH [Mon May 06 17:28:22 2024] passed all 5 tests [Mon May 06 17:28:22 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 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' in '../velvet_1.2.10+dfsg1-8_amd64.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-8_amd64.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-8_amd64.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-8_amd64.deb'. dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-8_all.deb'. dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-8_all.deb'. dpkg-genbuildinfo --build=binary -O../velvet_1.2.10+dfsg1-8_amd64.buildinfo dpkg-genchanges --build=binary -O../velvet_1.2.10+dfsg1-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/544435 and its subdirectories I: Current time: Mon May 6 05:28:57 -12 2024 I: pbuilder-time-stamp: 1715016537 Mon May 6 17:28:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Mon May 6 17:28:59 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Mon May 6 17:33:06 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Mon May 6 17:33:06 UTC 2024 I: velvet_1.2.10+dfsg1-8_amd64.changes: Format: 1.8 Date: Tue, 29 Nov 2022 20:22:14 +0100 Source: velvet Binary: velvet velvet-dbgsym velvet-example velvet-long velvet-long-dbgsym velvet-tests Architecture: amd64 all Version: 1.2.10+dfsg1-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille 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 Changes: velvet (1.2.10+dfsg1-8) unstable; urgency=medium . * Apply multi-arch hints. + velvet-tests: Add Multi-Arch: foreign. * Point Homepage to Github since original homepage vanished * Fix watch file * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * Fix typo in debian/rules rules: override_dh_auto_clean ⇒ override_dh_auto_clean, override_dh_auto_build ⇒ override_dh_auto_build, override_dh_install ⇒ override_dh_install, override_dh_install ⇒ override_mh_install, override_dh_compress ⇒ override_dh_compress Checksums-Sha1: 9536baed4283e84e03ef97d2ea935fc7ac800202 966416 velvet-dbgsym_1.2.10+dfsg1-8_amd64.deb 6232d2526fe79d15070fec40881b5e5efe4822fa 3331156 velvet-example_1.2.10+dfsg1-8_all.deb a4ca8f372dd5e547dc2aa60e093256a25a5be327 1928644 velvet-long-dbgsym_1.2.10+dfsg1-8_amd64.deb a8cd369759a42d588a192d133c072af4c67789b8 208104 velvet-long_1.2.10+dfsg1-8_amd64.deb e2ba8b8e3e930509463acbd31eb3d1d4fd536b41 10748796 velvet-tests_1.2.10+dfsg1-8_all.deb c5bd539c943836e62787207989783035fda5e9be 7922 velvet_1.2.10+dfsg1-8_amd64.buildinfo 0133b9d70792cd5a4081f7deef1e8500f886684f 676724 velvet_1.2.10+dfsg1-8_amd64.deb Checksums-Sha256: 08fa85fdb564cbed72c747a562664c0cc89a4e65229283b02fea0feef6ca1b4d 966416 velvet-dbgsym_1.2.10+dfsg1-8_amd64.deb 8d81ca43c779e1a467c4084a0ec8baafbc220f5d81b9e9219498a846ba5414de 3331156 velvet-example_1.2.10+dfsg1-8_all.deb 9136f493c199a812aff2d497d6b2dda031394a2e5c66ce415b8c795a8bf4754c 1928644 velvet-long-dbgsym_1.2.10+dfsg1-8_amd64.deb bc17076f06246e978b5ac8c8f9c536e4639bd4908f903bf056a9b19b097c7151 208104 velvet-long_1.2.10+dfsg1-8_amd64.deb 0ff42d46f1c50186a5c330eb754e9f1be94796cdff1fab5ed37c1fe0c36dcc9c 10748796 velvet-tests_1.2.10+dfsg1-8_all.deb 8fa776dcce369dd0f1bd94674472d7b8bbd11b8d5a4faf68789103cb219c603f 7922 velvet_1.2.10+dfsg1-8_amd64.buildinfo 951b8eda76c0d0bc9b6473f03eee95fa12fc3ebc7fa6a622f12412d73665dfaf 676724 velvet_1.2.10+dfsg1-8_amd64.deb Files: 4a65624932e5b75a407fe0222a689565 966416 debug optional velvet-dbgsym_1.2.10+dfsg1-8_amd64.deb 09fb602c715e0b69dedf026b7b906421 3331156 science optional velvet-example_1.2.10+dfsg1-8_all.deb 5abf7a1aae5d14c1dfefe99d825b3d1b 1928644 debug optional velvet-long-dbgsym_1.2.10+dfsg1-8_amd64.deb 127d0cb65f5b04be638a42b4badcdede 208104 science optional velvet-long_1.2.10+dfsg1-8_amd64.deb 4eaa3856e6960ae33805fb5accfd115f 10748796 science optional velvet-tests_1.2.10+dfsg1-8_all.deb 5bbcdc2d9b5f5396481f21a5478130fd 7922 science optional velvet_1.2.10+dfsg1-8_amd64.buildinfo ea894037dc94093d0af386bb03aaafe4 676724 science optional velvet_1.2.10+dfsg1-8_amd64.deb Mon May 6 17:33:08 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_33-11006.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tOESGjXd/velvet_1.2.10+dfsg1-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tOESGjXd/velvet_1.2.10+dfsg1-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tOESGjXd/velvet_1.2.10+dfsg1-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tOESGjXd/b1/velvet_1.2.10+dfsg1-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tOESGjXd/b2/velvet_1.2.10+dfsg1-8_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.543s) 0.543s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.202s) 0.202s 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: 874ms CPU time consumed: 875ms Mon May 6 17:33:09 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Mon May 6 17:33:09 UTC 2024 I: velvet from trixie built successfully and reproducibly on amd64. Mon May 6 17:33:10 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 6 17:33:10 UTC 2024 I: Submitting 12K b1/velvet_1.2.10+dfsg1-8_amd64.buildinfo.asc Mon May 6 17:33:11 UTC 2024 I: Submitting 12K b2/velvet_1.2.10+dfsg1-8_amd64.buildinfo.asc Mon May 6 17:33:12 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 6 17:33:12 UTC 2024 I: Done submitting .buildinfo files. Mon May 6 17:33:12 UTC 2024 I: Removing signed velvet_1.2.10+dfsg1-8_amd64.buildinfo.asc files: removed './b1/velvet_1.2.10+dfsg1-8_amd64.buildinfo.asc' removed './b2/velvet_1.2.10+dfsg1-8_amd64.buildinfo.asc'