sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | velvet 1.2.10+dfsg1-9 (i386) Sun, 20 Oct 2024 14:12:28 +0000 | +==============================================================================+ Package: velvet Version: 1.2.10+dfsg1-9 Source Version: 1.2.10+dfsg1-9 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.On58KWKka5... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-fUHev0/resolver-NXanyg' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [202 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [10.9 MB] Get:3 http://mirror.einval.org/debian unstable/main i386 Packages [9793 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 Packages [9926 kB] Fetched 30.8 MB in 8s (3991 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.7 MB of source archives. Get:1 http://mirror.einval.org/debian unstable/main velvet 1.2.10+dfsg1-9 (dsc) [2393 B] Get:2 http://mirror.einval.org/debian unstable/main velvet 1.2.10+dfsg1-9 (tar) [13.6 MB] Get:3 http://mirror.einval.org/debian unstable/main velvet 1.2.10+dfsg1-9 (diff) [18.5 kB] Fetched 13.7 MB in 0s (35.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/velvet-fUHev0/velvet-1.2.10+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-fUHev0' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [770 B] Get:5 copy:/<>/apt_archive ./ Packages [812 B] Fetched 2191 B in 0s (123 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-14-i686-linux-gnu cpp-i686-linux-gnu crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern g++-14-i686-linux-gnu g++-i686-linux-gnu gcc-14-base:i386 gcc-14-cross-base gcc-14-i686-linux-gnu gcc-14-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libbrotli1 libbsd0 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcairo2 libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-14-dev:i386 libgcc-14-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libglib2.0-0t64 libgomp1:i386 libgomp1-i386-cross libgraphite2-3 libharfbuzz0b libice6 libicu72 libitm1:i386 libitm1-i386-cross libkpathsea6 libmagic-mgc libmagic1t64 libmpfi0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libquadmath0:i386 libquadmath0-i386-cross libsm6 libstdc++-14-dev:i386 libstdc++-14-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsynctex2 libteckit0 libtexlua53-5 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 linux-libc-dev-i386-cross m4 man-db po-debconf sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils zlib1g:i386 zlib1g-dev:i386 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-14-locales cpp-14-doc cpp-doc dh-make gcc-14-doc manpages-dev flex bison gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:i386 libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386 manpages-dev:i386 low-memory-monitor libmpfi-doc libstdc++-14-doc:i386 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc wp2latex texlive-latex-recommended-doc texlive-luatex texlive-pstricks Recommended packages: curl | wget | lynx libidn2-0:i386 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl lmodern dvisvgm libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-14-i686-linux-gnu cpp-i686-linux-gnu crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern g++-14-i686-linux-gnu g++-i686-linux-gnu gcc-14-base:i386 gcc-14-cross-base gcc-14-i686-linux-gnu gcc-14-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libbrotli1 libbsd0 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcairo2 libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-14-dev:i386 libgcc-14-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libglib2.0-0t64 libgomp1:i386 libgomp1-i386-cross libgraphite2-3 libharfbuzz0b libice6 libicu72 libitm1:i386 libitm1-i386-cross libkpathsea6 libmagic-mgc libmagic1t64 libmpfi0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libquadmath0:i386 libquadmath0-i386-cross libsm6 libstdc++-14-dev:i386 libstdc++-14-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsynctex2 libteckit0 libtexlua53-5 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 linux-libc-dev-i386-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:i386 sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils zlib1g:i386 zlib1g-dev:i386 0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 149 MB of archives. After this operation, 548 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 gcc-14-i686-linux-gnu-base arm64 14.2.0-6cross1 [46.9 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 cpp-14-i686-linux-gnu arm64 14.2.0-6cross1 [10.4 MB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-i686-linux-gnu arm64 4:14.2.0-1 [4840 B] Get:21 http://mirror.einval.org/debian unstable/main arm64 binutils-i686-linux-gnu arm64 2.43.1-5 [2442 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14.2.0-6cross1 [42.2 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libc6-i386-cross all 2.40-3cross1 [1391 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-i386-cross all 14.2.0-6cross1 [88.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libgomp1-i386-cross all 14.2.0-6cross1 [135 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libitm1-i386-cross all 14.2.0-6cross1 [26.8 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libatomic1-i386-cross all 14.2.0-6cross1 [7368 B] Get:28 http://mirror.einval.org/debian unstable/main arm64 libasan8-i386-cross all 14.2.0-6cross1 [2600 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-i386-cross all 14.2.0-6cross1 [718 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libubsan1-i386-cross all 14.2.0-6cross1 [1054 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-i386-cross all 14.2.0-6cross1 [231 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libgcc-14-dev-i386-cross all 14.2.0-6cross1 [2581 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 gcc-14-i686-linux-gnu arm64 14.2.0-6cross1 [20.0 MB] Get:34 http://mirror.einval.org/debian unstable/main arm64 gcc-i686-linux-gnu arm64 4:14.2.0-1 [1444 B] Get:35 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-i386-cross all 6.11.2-1cross1 [2266 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-i386-cross all 2.40-3cross1 [1766 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libstdc++-14-dev-i386-cross all 14.2.0-6cross1 [2418 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 g++-14-i686-linux-gnu arm64 14.2.0-6cross1 [11.3 MB] Get:39 http://mirror.einval.org/debian unstable/main arm64 g++-i686-linux-gnu arm64 4:14.2.0-1 [1200 B] Get:40 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-i386 all 12.12 [3544 B] Get:41 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:47 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.36-1 [29.1 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.36-1 [74.4 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get:61 http://mirror.einval.org/debian unstable/main i386 gcc-14-base i386 14.2.0-7 [46.9 kB] Get:62 http://mirror.einval.org/debian unstable/main i386 libgcc-s1 i386 14.2.0-7 [88.2 kB] Get:63 http://mirror.einval.org/debian unstable/main i386 libc6 i386 2.40-3 [2673 kB] Get:64 http://mirror.einval.org/debian unstable/main i386 libasan8 i386 14.2.0-7 [2607 kB] Get:65 http://mirror.einval.org/debian unstable/main i386 libatomic1 i386 14.2.0-7 [7632 B] Get:66 http://mirror.einval.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-2 [129 kB] Get:68 http://mirror.einval.org/debian unstable/main i386 libcrypt1 i386 1:4.4.36-5 [95.5 kB] Get:69 http://mirror.einval.org/debian unstable/main i386 libcrypt-dev i386 1:4.4.36-5 [125 kB] Get:70 http://mirror.einval.org/debian unstable/main i386 libc6-dev i386 2.40-3 [1770 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get:86 http://mirror.einval.org/debian unstable/main i386 libgomp1 i386 14.2.0-7 [138 kB] Get:87 http://mirror.einval.org/debian unstable/main i386 libitm1 i386 14.2.0-7 [27.3 kB] Get:88 http://mirror.einval.org/debian unstable/main i386 libstdc++6 i386 14.2.0-7 [765 kB] Get:89 http://mirror.einval.org/debian unstable/main i386 libubsan1 i386 14.2.0-7 [1055 kB] Get:90 http://mirror.einval.org/debian unstable/main i386 libquadmath0 i386 14.2.0-7 [231 kB] Get:91 http://mirror.einval.org/debian unstable/main i386 libgcc-14-dev i386 14.2.0-7 [2581 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-1 [1409 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-4 [153 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-3 [34.1 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get:101 http://mirror.einval.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b1 [23.1 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-4 [47.9 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get:104 http://mirror.einval.org/debian unstable/main i386 libstdc++-14-dev i386 14.2.0-7 [2436 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-4 [60.2 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1 [300 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-4 [106 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-4 [7373 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 texlive-base all 2024.20240829-2 [22.7 MB] Get:119 http://mirror.einval.org/debian unstable/main arm64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get:121 http://mirror.einval.org/debian unstable/main i386 zlib1g i386 1:1.3.dfsg+really1.3.1-1 [83.9 kB] Get:122 http://mirror.einval.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 149 MB in 2s (84.9 MB/s) Selecting previously unselected package sensible-utils. 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Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up gcc-14-i686-linux-gnu-base:arm64 (14.2.0-6cross1) ... Setting up gcc-14-cross-base (14.2.0-6cross1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:arm64 (1.36-1) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up linux-libc-dev-i386-cross (6.11.2-1cross1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-1) ... No schema files found: doing nothing. Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:arm64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:arm64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-4) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libc6-i386-cross (2.40-3cross1) ... Setting up fonts-lmodern (2.005-1) ... Setting up cpp-14-i686-linux-gnu (14.2.0-6cross1) ... Setting up libbsd0:arm64 (0.12.2-2) ... Setting up libquadmath0-i386-cross (14.2.0-6cross1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-4) ... Setting up libpotrace0:arm64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libatomic1-i386-cross (14.2.0-6cross1) ... Setting up libxcb-render0:arm64 (1.17.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libgomp1-i386-cross (14.2.0-6cross1) ... Setting up libxcb-shm0:arm64 (1.17.0-2) ... Setting up libc6-dev-i386-cross (2.40-3cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libgcc-s1-i386-cross (14.2.0-6cross1) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:arm64 (2024.20240313.70630+ds-4) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libitm1-i386-cross (14.2.0-6cross1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up cpp-i686-linux-gnu (4:14.2.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up libpaper1:arm64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxpm4:arm64 (1:3.5.17-1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libasan8-i386-cross (14.2.0-6cross1) ... Setting up libstdc++6-i386-cross (14.2.0-6cross1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libxmu6:arm64 (2:1.1.3-3+b2) ... Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up debhelper (13.20) ... Setting up libubsan1-i386-cross (14.2.0-6cross1) ... Setting up libxaw7:arm64 (2:1.0.14-1+b2) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240829-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libgcc-14-dev-i386-cross (14.2.0-6cross1) ... Setting up texlive-latex-base (2024.20240829-2) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Setting up gcc-14-i686-linux-gnu (14.2.0-6cross1) ... Setting up gcc-i686-linux-gnu (4:14.2.0-1) ... Setting up libstdc++-14-dev-i386-cross (14.2.0-6cross1) ... Setting up g++-14-i686-linux-gnu (14.2.0-6cross1) ... Setting up g++-i686-linux-gnu (4:14.2.0-1) ... Setting up crossbuild-essential-i386 (12.12) ... Setting up libgcc-s1:i386 (14.2.0-7) ... Setting up libc6:i386 (2.40-3) ... Setting up libasan8:i386 (14.2.0-7) ... Setting up libstdc++6:i386 (14.2.0-7) ... Setting up libitm1:i386 (14.2.0-7) ... Setting up zlib1g:i386 (1:1.3.dfsg+really1.3.1-1) ... Setting up libcrypt1:i386 (1:4.4.36-5) ... Setting up libgomp1:i386 (14.2.0-7) ... Setting up libquadmath0:i386 (14.2.0-7) ... Setting up libatomic1:i386 (14.2.0-7) ... Setting up libubsan1:i386 (14.2.0-7) ... Setting up libcrypt-dev:i386 (1:4.4.36-5) ... Setting up libc6-dev:i386 (2.40-3) ... Setting up libgcc-14-dev:i386 (14.2.0-7) ... Setting up libstdc++-14-dev:i386 (14.2.0-7) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-25-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) arm64 (aarch64) Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-7 gcc-14_14.2.0-7 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-7 libstdc++-14-dev-i386-cross_14.2.0-6cross1 libstdc++6_14.2.0-7 libstdc++6-i386-cross_14.2.0-6cross1 linux-libc-dev_6.11.2-1 Package versions: apt_2.9.9 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 binutils-i686-linux-gnu_2.43.1-5 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.2.0-1 cpp-14_14.2.0-7 cpp-14-aarch64-linux-gnu_14.2.0-7 cpp-14-i686-linux-gnu_14.2.0-6cross1 cpp-aarch64-linux-gnu_4:14.2.0-1 cpp-i686-linux-gnu_4:14.2.0-1 crossbuild-essential-i386_12.12 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 g++_4:14.2.0-1 g++-14_14.2.0-7 g++-14-aarch64-linux-gnu_14.2.0-7 g++-14-i686-linux-gnu_14.2.0-6cross1 g++-aarch64-linux-gnu_4:14.2.0-1 g++-i686-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-7 gcc-14-aarch64-linux-gnu_14.2.0-7 gcc-14-base_14.2.0-7 gcc-14-cross-base_14.2.0-6cross1 gcc-14-i686-linux-gnu_14.2.0-6cross1 gcc-14-i686-linux-gnu-base_14.2.0-6cross1 gcc-aarch64-linux-gnu_4:14.2.0-1 gcc-i686-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 gpgv_2.2.44-1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.25 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.9 libarchive-zip-perl_1.68-1 libasan8_14.2.0-7 libasan8-i386-cross_14.2.0-6cross1 libatomic1_14.2.0-7 libatomic1-i386-cross_14.2.0-6cross1 libattr1_1:2.5.2-2 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-5 libblkid1_2.40.2-9 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-3 libc-dev-bin_2.40-3 libc6_2.40-3 libc6-dev_2.40-3 libc6-dev-i386-cross_2.40-3cross1 libc6-i386-cross_2.40-3cross1 libcairo2_1.18.2-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-7 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libelf1t64_0.191-2 libexpat1_2.6.3-1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libfontconfig1_2.15.0-1.1 libfreetype6_2.13.3+dfsg-1 libgcc-14-dev_14.2.0-7 libgcc-14-dev-i386-cross_14.2.0-6cross1 libgcc-s1_14.2.0-7 libgcc-s1-i386-cross_14.2.0-6cross1 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libglib2.0-0t64_2.82.2-1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-7 libgomp1-i386-cross_14.2.0-6cross1 libgpg-error0_1.50-4 libgprofng0_2.43.1-5 libgraphite2-3_1.3.14-2 libharfbuzz0b_10.0.1-1 libhogweed6t64_3.10-1 libhwasan0_14.2.0-7 libice6_2:1.0.10-1+b1 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.27-1 libitm1_14.2.0-7 libitm1-i386-cross_14.2.0-6cross1 libjansson4_2.14-2+b2 libkpathsea6_2024.20240313.70630+ds-4 liblsan0_14.2.0-7 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-9 libmpc3_1.3.1-1+b2 libmpfi0_1.5.4+ds-3 libmpfr6_4.2.1-1+b1 libnettle8t64_3.10-1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpaper-utils_1.1.29+b1 libpaper1_1.1.29+b1 libpcre2-8-0_10.42-4+b1 libperl5.40_5.40.0-6 libpipeline1_1.5.8-1 libpixman-1-0_0.42.2-1+b1 libpng16-16t64_1.6.44-2 libpotrace0_1.16-2+b1 libptexenc1_2024.20240313.70630+ds-4 libquadmath0_14.2.0-7 libquadmath0-i386-cross_14.2.0-6cross1 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsframe1_2.43.1-5 libsm6_2:1.2.3-1+b1 libsmartcols1_2.40.2-9 libssl3t64_3.3.2-1 libstdc++-14-dev_14.2.0-7 libstdc++-14-dev-i386-cross_14.2.0-6cross1 libstdc++6_14.2.0-7 libstdc++6-i386-cross_14.2.0-6cross1 libsynctex2_2024.20240313.70630+ds-4 libsystemd0_256.7-2 libtasn1-6_4.19.0-3+b2 libteckit0_2.5.12+ds1-1 libtexlua53-5_2024.20240313.70630+ds-4 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-7 libubsan1_14.2.0-7 libubsan1-i386-cross_14.2.0-6cross1 libuchardet0_0.0.8-1+b1 libudev1_256.7-2 libunistring5_1.2-1 libuuid1_2.40.2-9 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxaw7_2:1.0.14-1+b2 libxcb-render0_1.17.0-2 libxcb-shm0_1.17.0-2 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxext6_2:1.3.4-1+b2 libxi6_2:1.8.2-1 libxml2_2.12.7+dfsg+really2.9.14-0.1 libxmu6_2:1.1.3-3+b2 libxpm4_1:3.5.17-1+b1 libxrender1_1:0.9.10-1.1+b1 libxt6t64_1:1.2.1-1.2 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 libzzip-0-13t64_0.13.72+dfsg.1-1.3 linux-libc-dev_6.11.2-1 linux-libc-dev-i386-cross_6.11.2-1cross1 login_1:4.16.0-2+really2.40.2-9 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 openssl-provider-legacy_3.3.2-1 patch_2.7.6-7 perl_5.40.0-6 perl-base_5.40.0-6 perl-modules-5.40_5.40.0-6 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-3 t1utils_1.41-4 tar_1.35+dfsg-3 tex-common_6.18 texlive-base_2024.20240829-2 texlive-binaries_2024.20240313.70630+ds-4 texlive-latex-base_2024.20240829-2 texlive-latex-recommended_2024.20240829-2 ucf_3.0043+nmu1 util-linux_2.40.2-9 x11-common_1:7.7+23.1 xdg-utils_1.1.3-4.1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: velvet Binary: velvet, velvet-long, velvet-example, velvet-tests Architecture: any all Version: 1.2.10+dfsg1-9 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/dzerbino/velvet Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/velvet Vcs-Git: https://salsa.debian.org/med-team/velvet.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended Package-List: velvet deb science optional arch=any velvet-example deb science optional arch=all velvet-long deb science optional arch=any velvet-tests deb science optional arch=all Checksums-Sha1: f5ade530e902bdf69532648429a91c00f3a1ad2d 13630488 velvet_1.2.10+dfsg1.orig.tar.xz a90ae2c99b8e907d21ea487acced5450df59e5ec 18476 velvet_1.2.10+dfsg1-9.debian.tar.xz Checksums-Sha256: 368d760ad56ffa010a2ae72b25d46680ecb7ad8cc573cf6c389848c87b32ee26 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 6d34641dd5a1fec20bb47508d3e2e045cd06a0e73dbeda44e38c90be0b135183 18476 velvet_1.2.10+dfsg1-9.debian.tar.xz Files: 7a58a6d75cdc8b89d1c605033050bbcf 13630488 velvet_1.2.10+dfsg1.orig.tar.xz a40a683daca2441b5ded8972fbe1508b 18476 velvet_1.2.10+dfsg1-9.debian.tar.xz Dgit: 89cc29c026c11e5aeb7087d5bc0b483a4b20195c debian archive/debian/1.2.10+dfsg1-9 https://git.dgit.debian.org/velvet -----BEGIN PGP SIGNATURE----- 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signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-9.dsc: no acceptable signature found dpkg-source: info: extracting velvet in /<> dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying gcc-14.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.i386 DEB_BUILD_OPTIONS=nocheck HOME=/var/lib/sbuild LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -ai386 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-architecture: warning: specified GNU system type i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' 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 '/<>' 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 '/<>' dh_clean debian/rules binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Manual.aux. 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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 331. Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 354. LaTeX Warning: Reference `sec:kmercov' on page 8 undefined on input line 358. LaTeX Warning: Reference `sec:expcov' on page 8 undefined on input line 358. Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [8] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] LaTeX Warning: Reference `sec:hashing' on page 9 undefined on input line 377. LaTeX Warning: Reference `sec:kmercov' on page 9 undefined on input line 379. LaTeX Warning: Reference `sec:pairedformat' on page 9 undefined on input line 3 95. Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [9] [10] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:amos' on page 11 undefined on input line 455. Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 11 undefined on input line 470. Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set LaTeX Warning: Reference `sec:paper' on page 11 undefined on input line 499. [11] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [12] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [13] LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 593. LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 605. Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 615. [14] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 642. Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 683 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 695. LaTeX Warning: Reference `sec:kmercov' on page 16 undefined on input line 695. [16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /<>/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) >/velv et-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk> Output written on Manual.pdf (21 pages, 432098 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./Manual.out ) (./Manual.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota l 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, tota l 100165,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, tota l 100122,[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 59--59 [] \OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] [6] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov [15] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [16] [17] [18 <./Suis_plot_1.pdf>] [19 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [20] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [21] [22] (./Manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) >/velv et-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk> Output written on Manual.pdf (22 pages, 440025 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-08-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (29.9002pt too wide) in paragraph at lines 145--145 [] \OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_sequ ences.fa[] [5] (./Columbus_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /<>/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. ) (see the transcript file for additional information) >/velv et-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk> Output written on Columbus_manual.pdf (5 pages, 88603 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/<>' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' 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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function ‘collectReferenceCoords’: src/graphStats.c:1961:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=] 1961 | sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long int | %lld In file included from src/graphStats.c:28: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function ‘importCnyReadSet’: src/binarySequences.c:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ^ src/binarySequences.c:304:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c:304:67: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/binarySequences.c:304:84: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 304 | velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int long long unsigned int | %llx src/binarySequences.c: In function ‘moveCnySeqNucleotides’: src/binarySequences.c:389:36: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 389 | velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); | ~~^ ~~~~~~ | | | | long int uint64_t {aka long long unsigned int} | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function ‘createPreNodes’: src/preGraphConstruction.c:525:72: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld src/preGraphConstruction.c:525:94: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 525 | velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int long long unsigned int | %lld i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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; | ^~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:17: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | dup(out[1]); | ^~~~~~~~~~~ i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>' make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -X.pdf -X.c -X.pl -X.h -X.xz make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-9_i386.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-9_i386.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-9_i386.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-9_i386.deb'. dpkg-genbuildinfo --build=any -O../velvet_1.2.10+dfsg1-9_i386.buildinfo dpkg-genchanges --build=any -O../velvet_1.2.10+dfsg1-9_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-10-20T14:22:50Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ velvet_1.2.10+dfsg1-9_i386.changes: ----------------------------------- Format: 1.8 Date: Wed, 07 Aug 2024 11:51:33 +0200 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Built-For-Profiles: cross nocheck Architecture: i386 Version: 1.2.10+dfsg1-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: velvet - Nucleic acid sequence assembler for very short reads velvet-long - Nucleic acid sequence assembler for very short reads, long versio Closes: 1075617 Changes: velvet (1.2.10+dfsg1-9) unstable; urgency=medium . * Team upload. * gcc-14.patch: new: fix incompatible pointer types. (Closes: #1075617) * d/control: declare compliance to standards version 4.7.0. * hardening.patch: also propagate CPPFLAGS. This allows fortifying the source where applicable. 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arm64 Build-Date: Sun, 20 Oct 2024 14:22:49 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-5), binutils-aarch64-linux-gnu (= 2.43.1-5), binutils-common (= 2.43.1-5), bsdextrautils (= 2.40.2-9), bsdutils (= 1:2.40.2-9), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-7), cpp-14-aarch64-linux-gnu (= 14.2.0-7), cpp-aarch64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), fontconfig-config (= 2.15.0-1.1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-7), g++-14-aarch64-linux-gnu (= 14.2.0-7), g++-aarch64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-7), gcc-14-aarch64-linux-gnu (= 14.2.0-7), gcc-14-base (= 14.2.0-7), gcc-aarch64-linux-gnu (= 4:14.2.0-1), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.25), init-system-helpers (= 1.67), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-7), libatomic1 (= 14.2.0-7), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbinutils (= 2.43.1-5), libblkid1 (= 2.40.2-9), libbrotli1 (= 1.1.0-2+b4), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-3), libc-dev-bin (= 2.40-3), libc6 (= 2.40-3), libc6-dev (= 2.40-3), libcairo2 (= 1.18.2-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-7), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-5), libctf0 (= 2.43.1-5), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexpat1 (= 2.6.3-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfontconfig1 (= 2.15.0-1.1), libfreetype6 (= 2.13.3+dfsg-1), libgcc-14-dev (= 14.2.0-7), libgcc-s1 (= 14.2.0-7), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libglib2.0-0t64 (= 2.82.2-1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-7), libgprofng0 (= 2.43.1-5), libgraphite2-3 (= 1.3.14-2), libharfbuzz0b (= 10.0.1-1), libhwasan0 (= 14.2.0-7), libice6 (= 2:1.0.10-1+b1), libicu72 (= 72.1-5), libisl23 (= 0.27-1), libitm1 (= 14.2.0-7), libjansson4 (= 2.14-2+b2), libkpathsea6 (= 2024.20240313.70630+ds-4), liblsan0 (= 14.2.0-7), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-9), libmpc3 (= 1.3.1-1+b2), libmpfi0 (= 1.5.4+ds-3), libmpfr6 (= 4.2.1-1+b1), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpaper-utils (= 1.1.29+b1), libpaper1 (= 1.1.29+b1), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-6), libpipeline1 (= 1.5.8-1), libpixman-1-0 (= 0.42.2-1+b1), libpng16-16t64 (= 1.6.44-2), libpotrace0 (= 1.16-2+b1), libptexenc1 (= 2024.20240313.70630+ds-4), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-5), libsm6 (= 2:1.2.3-1+b1), libsmartcols1 (= 2.40.2-9), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-7), libstdc++6 (= 14.2.0-7), libsynctex2 (= 2024.20240313.70630+ds-4), libsystemd0 (= 256.7-2), libteckit0 (= 2.5.12+ds1-1), libtexlua53-5 (= 2024.20240313.70630+ds-4), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-7), libubsan1 (= 14.2.0-7), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.7-2), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-9), libx11-6 (= 2:1.8.7-1+b1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1+b1), libxaw7 (= 2:1.0.14-1+b2), libxcb-render0 (= 1.17.0-2), libxcb-shm0 (= 1.17.0-2), libxcb1 (= 1.17.0-2), libxdmcp6 (= 1:1.1.2-3+b1), libxext6 (= 2:1.3.4-1+b2), libxi6 (= 2:1.8.2-1), libxml2 (= 2.12.7+dfsg+really2.9.14-0.1), libxmu6 (= 2:1.1.3-3+b2), libxpm4 (= 1:3.5.17-1+b1), libxrender1 (= 1:0.9.10-1.1+b1), libxt6t64 (= 1:1.2.1-1.2), libzstd1 (= 1.5.6+dfsg-1), libzzip-0-13t64 (= 0.13.72+dfsg.1-1.3), linux-libc-dev (= 6.11.2-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-6), perl-base (= 5.40.0-6), perl-modules-5.40 (= 5.40.0-6), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-3), t1utils (= 1.41-4), tar (= 1.35+dfsg-3), tex-common (= 6.18), texlive-base (= 2024.20240829-2), texlive-binaries (= 2024.20240313.70630+ds-4), texlive-latex-base (= 2024.20240829-2), texlive-latex-recommended (= 2024.20240829-2), ucf (= 3.0043+nmu1), util-linux (= 2.40.2-9), x11-common (= 1:7.7+23.1), xdg-utils (= 1.1.3-4.1), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1723024293" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ velvet-dbgsym_1.2.10+dfsg1-9_i386.deb ------------------------------------- new Debian package, version 2.0. size 902944 bytes: control archive=748 bytes. 502 bytes, 12 lines control 505 bytes, 5 lines md5sums Package: velvet-dbgsym Source: velvet Version: 1.2.10+dfsg1-9 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 977 Depends: velvet (= 1.2.10+dfsg1-9) Section: debug Priority: optional Description: debug symbols for velvet Build-Ids: 2326555fab43bbc976ea1812c28b8e2fcc1ed784 30dfceec4515c76e08c21e5ad7dc5f7f5c367b2b ec8d278b4ed343e10c7146a7d906dde84300e75c f58189405c2b7827f15dca6eea2527b6f78440f7 drwxr-xr-x root/root 0 2024-08-07 09:51 ./ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/23/ -rw-r--r-- root/root 96628 2024-08-07 09:51 ./usr/lib/debug/.build-id/23/26555fab43bbc976ea1812c28b8e2fcc1ed784.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/30/ -rw-r--r-- root/root 371732 2024-08-07 09:51 ./usr/lib/debug/.build-id/30/dfceec4515c76e08c21e5ad7dc5f7f5c367b2b.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/ec/ -rw-r--r-- root/root 99268 2024-08-07 09:51 ./usr/lib/debug/.build-id/ec/8d278b4ed343e10c7146a7d906dde84300e75c.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/f5/ -rw-r--r-- root/root 371660 2024-08-07 09:51 ./usr/lib/debug/.build-id/f5/8189405c2b7827f15dca6eea2527b6f78440f7.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.dwz/i386-linux-gnu/ -rw-r--r-- root/root 43148 2024-08-07 09:51 ./usr/lib/debug/.dwz/i386-linux-gnu/velvet.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-07 09:51 ./usr/share/doc/velvet-dbgsym -> velvet velvet-long-dbgsym_1.2.10+dfsg1-9_i386.deb ------------------------------------------ new Debian package, version 2.0. size 1769608 bytes: control archive=1044 bytes. 764 bytes, 12 lines control 1146 bytes, 11 lines md5sums Package: velvet-long-dbgsym Source: velvet Version: 1.2.10+dfsg1-9 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 2359 Depends: velvet-long (= 1.2.10+dfsg1-9) Section: debug Priority: optional Description: debug symbols for velvet-long Build-Ids: 2895700050bc1eff82414d1803a7835554bfda8c 439df57236d66cbfc11f0508eec190b704de30ad 5d1e1e901df47f5b97754b5fae681e6eeda4303e 8375426935c8ecc05ff8fe38245fc1eba12872ff c5e8e3f7963a19065e42055019eb46824722d1fa c6f98766dbbd6675077977c6d5dfac11e4c0d772 dc91acf159aebf55f2db99519ec003962ef440fc ded1cb9e0d34c6183649d384258456f180d84bb8 ef2ce0558a41a1a527b9c5bff8e86ee5eee02f98 f0c2556cb58e0d5b6180ab3ed63b9e189e52d18d drwxr-xr-x root/root 0 2024-08-07 09:51 ./ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 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root/root 372104 2024-08-07 09:51 ./usr/lib/debug/.build-id/c6/f98766dbbd6675077977c6d5dfac11e4c0d772.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/dc/ -rw-r--r-- root/root 371632 2024-08-07 09:51 ./usr/lib/debug/.build-id/dc/91acf159aebf55f2db99519ec003962ef440fc.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/de/ -rw-r--r-- root/root 371248 2024-08-07 09:51 ./usr/lib/debug/.build-id/de/d1cb9e0d34c6183649d384258456f180d84bb8.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/ef/ -rw-r--r-- root/root 96920 2024-08-07 09:51 ./usr/lib/debug/.build-id/ef/2ce0558a41a1a527b9c5bff8e86ee5eee02f98.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/f0/ -rw-r--r-- root/root 96580 2024-08-07 09:51 ./usr/lib/debug/.build-id/f0/c2556cb58e0d5b6180ab3ed63b9e189e52d18d.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.dwz/i386-linux-gnu/ -rw-r--r-- root/root 44848 2024-08-07 09:51 ./usr/lib/debug/.dwz/i386-linux-gnu/velvet-long.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-07 09:51 ./usr/share/doc/velvet-long-dbgsym -> velvet-long velvet-long_1.2.10+dfsg1-9_i386.deb ----------------------------------- new Debian package, version 2.0. size 233348 bytes: control archive=1452 bytes. 998 bytes, 22 lines control 1499 bytes, 23 lines md5sums Package: velvet-long Source: velvet Version: 1.2.10+dfsg1-9 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 2369 Depends: libc6 (>= 2.34), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2), velvet Section: science Priority: optional Homepage: https://github.com/dzerbino/velvet Description: Nucleic acid sequence assembler for very short reads, long version Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. . This package installs special long-mode versions of Velvet, as recommended in the Velvet tutorials. drwxr-xr-x root/root 0 2024-08-07 09:51 ./ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/bin/ -rwxr-xr-x root/root 362572 2024-08-07 09:51 ./usr/bin/velvetg_127 -rwxr-xr-x root/root 362572 2024-08-07 09:51 ./usr/bin/velvetg_127_long -rwxr-xr-x root/root 362572 2024-08-07 09:51 ./usr/bin/velvetg_63 -rwxr-xr-x root/root 362572 2024-08-07 09:51 ./usr/bin/velvetg_63_long -rwxr-xr-x root/root 362560 2024-08-07 09:51 ./usr/bin/velvetg_long -rwxr-xr-x root/root 112644 2024-08-07 09:51 ./usr/bin/velveth_127 -rwxr-xr-x root/root 112644 2024-08-07 09:51 ./usr/bin/velveth_127_long -rwxr-xr-x root/root 112644 2024-08-07 09:51 ./usr/bin/velveth_63 -rwxr-xr-x root/root 112644 2024-08-07 09:51 ./usr/bin/velveth_63_long -rwxr-xr-x root/root 112632 2024-08-07 09:51 ./usr/bin/velveth_long drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc/velvet-long/ -rw-r--r-- root/root 952 2024-08-07 09:51 ./usr/share/doc/velvet-long/changelog.Debian.gz -rw-r--r-- root/root 4572 2013-06-06 20:00 ./usr/share/doc/velvet-long/changelog.gz -rw-r--r-- root/root 4436 2024-08-07 09:51 ./usr/share/doc/velvet-long/copyright drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/man/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/man/man1/ -rw-r--r-- root/root 1488 2024-08-07 09:51 ./usr/share/man/man1/velvetg_127.1.gz -rw-r--r-- root/root 1508 2024-08-07 09:51 ./usr/share/man/man1/velvetg_127_long.1.gz -rw-r--r-- root/root 1487 2024-08-07 09:51 ./usr/share/man/man1/velvetg_63.1.gz -rw-r--r-- root/root 1507 2024-08-07 09:51 ./usr/share/man/man1/velvetg_63_long.1.gz -rw-r--r-- root/root 1483 2024-08-07 09:51 ./usr/share/man/man1/velvetg_long.1.gz -rw-r--r-- root/root 1442 2024-08-07 09:51 ./usr/share/man/man1/velveth_127.1.gz -rw-r--r-- root/root 1463 2024-08-07 09:51 ./usr/share/man/man1/velveth_127_long.1.gz -rw-r--r-- root/root 1441 2024-08-07 09:51 ./usr/share/man/man1/velveth_63.1.gz -rw-r--r-- root/root 1462 2024-08-07 09:51 ./usr/share/man/man1/velveth_63_long.1.gz -rw-r--r-- root/root 1454 2024-08-07 09:51 ./usr/share/man/man1/velveth_long.1.gz velvet_1.2.10+dfsg1-9_i386.deb ------------------------------ new Debian package, version 2.0. size 685380 bytes: control archive=1324 bytes. 876 bytes, 19 lines control 1161 bytes, 18 lines md5sums Package: velvet Version: 1.2.10+dfsg1-9 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 1483 Depends: libc6 (>= 2.34), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2) Suggests: velvet-example Section: science Priority: optional Homepage: https://github.com/dzerbino/velvet Description: Nucleic acid sequence assembler for very short reads Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. drwxr-xr-x root/root 0 2024-08-07 09:51 ./ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/bin/ -rwxr-xr-x root/root 362552 2024-08-07 09:51 ./usr/bin/velvetg -rwxr-xr-x root/root 362552 2024-08-07 09:51 ./usr/bin/velvetg_de -rwxr-xr-x root/root 112624 2024-08-07 09:51 ./usr/bin/velveth -rwxr-xr-x root/root 112624 2024-08-07 09:51 ./usr/bin/velveth_de drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc-base/ -rw-r--r-- root/root 243 2024-08-07 09:51 ./usr/share/doc-base/velvet.velvet drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/doc/velvet/ -rw-r--r-- root/root 1956 2013-06-06 20:00 ./usr/share/doc/velvet/CREDITS.txt -rw-r--r-- root/root 88603 2024-08-07 09:51 ./usr/share/doc/velvet/Columbus_manual.pdf -rw-r--r-- root/root 440025 2024-08-07 09:51 ./usr/share/doc/velvet/Manual.pdf -rw-r--r-- root/root 220 2024-08-07 09:51 ./usr/share/doc/velvet/README.Debian -rw-r--r-- root/root 405 2024-08-07 09:51 ./usr/share/doc/velvet/README.test -rw-r--r-- root/root 1117 2013-06-06 20:00 ./usr/share/doc/velvet/README.txt -rw-r--r-- root/root 949 2024-08-07 09:51 ./usr/share/doc/velvet/changelog.Debian.gz -rw-r--r-- root/root 4572 2013-06-06 20:00 ./usr/share/doc/velvet/changelog.gz -rw-r--r-- root/root 4436 2024-08-07 09:51 ./usr/share/doc/velvet/copyright drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/man/ drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/share/man/man1/ -rw-r--r-- root/root 1460 2024-08-07 09:51 ./usr/share/man/man1/velvetg.1.gz -rw-r--r-- root/root 1479 2024-08-07 09:51 ./usr/share/man/man1/velvetg_de.1.gz -rw-r--r-- root/root 1422 2024-08-07 09:51 ./usr/share/man/man1/velveth.1.gz -rw-r--r-- root/root 1453 2024-08-07 09:51 ./usr/share/man/man1/velveth_de.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1352 B] Get:5 copy:/<>/apt_archive ./ Packages [1429 B] Fetched 3396 B in 0s (179 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libgssapi-krb5-2 libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libpsl5t64 libreadline8t64 libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common shared-mime-info unzip Suggested packages: apt-config-icons isoquery libxml-parser-perl krb5-doc krb5-user libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl krb5-locales libldap-common liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl publicsuffix libsasl2-modules libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl The following NEW packages will be installed: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libgssapi-krb5-2 libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libpsl5t64 libreadline8t64 libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:i386 shared-mime-info unzip 0 upgraded, 157 newly installed, 0 to remove and 0 not upgraded. Need to get 16.5 MB of archives. After this operation, 72.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b1 [755 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get:11 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.10.1-2 [328 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libstemmer0d arm64 2.2.0-4+b1 [112 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libxmlb2 arm64 0.3.21-1 [59.1 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libappstream5 arm64 1.0.3-1 [207 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 appstream arm64 1.0.3-1 [466 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.66-1 [31.6 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libassuan9 arm64 3.0.1-2 [58.1 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.2.44-1 [113 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.46.1-1 [852 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.2.44-1 [478 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.17.0-1 [3055 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.40+b6 [63.8 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:46 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.66-1 [115 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.66-1 [217 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:55 http://mirror.einval.org/debian unstable/main arm64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:65 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.38-1+b1 [127 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.60-1 [41.8 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-1+b4 [31.2 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-4 [31.5 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.15-1 [11.9 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b4 [97.7 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.84-1+b1 [24.1 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b4 [28.2 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libnumber-compare-perl all 0.03-3 [6332 B] Get:85 http://mirror.einval.org/debian unstable/main arm64 libtext-glob-perl all 0.11-3 [7676 B] Get:86 http://mirror.einval.org/debian unstable/main arm64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.11-2 [31.4 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get:102 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-1+b2 [323 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.15~pre1-1 [37.7 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3 [48.9 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2+b1 [33.2 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:125 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.11-1+b1 [141 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB] Get:128 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.27-1+b3 [12.4 kB] Get:129 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:130 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get:131 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b4 [17.4 kB] Get:132 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b3 [11.4 kB] Get:133 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.636-1+b3 [41.7 kB] Get:134 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:135 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b3 [96.7 kB] Get:136 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b3 [99.0 kB] Get:137 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:138 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.46-1+b1 [63.6 kB] Get:139 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.30-1+b1 [27.1 kB] Get:140 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB] Get:141 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b4 [8772 B] Get:142 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.16-1+b3 [13.1 kB] Get:143 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2+b1 [172 kB] Get:144 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:145 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b4 [72.0 kB] Get:146 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-2+b3 [20.1 kB] Get:147 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.19-1 [114 kB] Get:148 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:149 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:150 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:151 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-5+b1 [300 kB] Get:152 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.902.0+ds-2+b1 [33.9 kB] Get:153 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.11-2 [58.9 kB] Get:154 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:155 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:156 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get:157 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.119.0 [1056 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.5 MB in 0s (54.1 MB/s) Selecting previously unselected package netbase. 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Unpacking sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b6) ... Setting up liblz1:arm64 (1.15~pre1-1) ... Setting up libberkeleydb-perl:arm64 (0.66-1) ... Setting up plzip (1.11-2) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libunicode-utf8-perl (0.62-2+b3) ... Setting up libmouse-perl:arm64 (2.5.11-1+b1) ... Setting up libdata-messagepack-perl (1.02-1+b4) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up libsub-identify-perl (0.14-3+b3) ... Setting up libcpanel-json-xs-perl:arm64 (4.38-1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxmlb2:arm64 (0.3.21-1) ... Setting up libdevel-size-perl (0.84-1+b1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:arm64 (3.46.1-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.902.0+ds-2+b1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.63.0-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up liblzo2-2:arm64 (2.10-3) ... Setting up libtime-moment-perl (0.44-2+b4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1+b3) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b4) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-4) ... Setting up libperlio-utf8-strict-perl (0.010-1+b3) ... Setting up shared-mime-info (2.4-5+b1) ... Setting up diffstat (1.66-1) ... Setting up libvariable-magic-perl (0.64-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:arm64 (3.5.9-2+b1) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:arm64 (0.27-1+b3) ... Setting up libdata-validate-domain-perl (0.15-1) ... Setting up libproc-processtable-perl:arm64 (0.636-1+b3) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up lzop (1.04-2) ... Setting up libassuan9:arm64 (3.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.049-1) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libfile-sharedir-perl (1.118-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libstemmer0d:arm64 (2.2.0-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.3.2-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b4) ... Setting up libperlio-gzip-perl (0.20-1+b4) ... Setting up readline-common (8.2-5) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b3) ... Setting up libmarkdown2:arm64 (2.2.7-2+b1) ... Setting up liburi-perl (5.30-1) ... Setting up iso-codes (4.17.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b4) ... Setting up libnet-ssleay-perl:arm64 (1.94-1+b2) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1+b3) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-3) ... Setting up libxs-parse-keyword-perl (0.46-1+b1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libwww-robotrules-perl (6.02-1) ... Setting up libsyntax-keyword-try-perl (0.30-1+b1) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b1) ... Setting up gpgconf (2.2.44-1) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.44-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhtml-form-perl (6.11-2) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libcgi-pm-perl (4.66-1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-2) ... Setting up libappstream5:arm64 (1.0.3-1) ... Setting up appstream (1.0.3-1) ... ✔ Metadata cache was updated successfully. Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.60-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.19-1) ... Setting up lintian (2.119.0) ... Setting up sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 79840 Build-Time: 365 Distribution: unstable Foreign Architectures: i386 Host Architecture: i386 Install-Time: 218 Job: velvet_1.2.10+dfsg1-9 Lintian: pass Machine Architecture: arm64 Package: velvet Package-Time: 622 Source-Version: 1.2.10+dfsg1-9 Space: 79840 Status: successful Version: 1.2.10+dfsg1-9 -------------------------------------------------------------------------------- Finished at 2024-10-20T14:22:50Z Build needed 00:10:22, 79840k disk space