sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | velvet 1.2.10+dfsg1-9 (armel) Tue, 29 Oct 2024 10:21:06 +0000 | +==============================================================================+ Package: velvet Version: 1.2.10+dfsg1-9 Source Version: 1.2.10+dfsg1-9 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-1ba71eb3-cf2a-4f6e-af79-200b8bfd819f' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-Nca9HA/resolver-I1M36k' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [202 kB] Get:2 http://localhost:3142/debian unstable/main Sources [10.9 MB] Get:3 http://localhost:3142/debian unstable/non-free-firmware Sources [7072 B] Get:4 http://localhost:3142/debian unstable/non-free Sources [83.7 kB] Get:5 http://localhost:3142/debian unstable/contrib Sources [61.9 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages [10.0 MB] Get:7 http://localhost:3142/debian unstable/main armel Packages [9478 kB] Fetched 30.7 MB in 3s (11.8 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-passwd bash coreutils cpp-14 cpp-14-x86-64-linux-gnu e2fsprogs g++-14 g++-14-x86-64-linux-gnu gcc-14 gcc-14-base gcc-14-x86-64-linux-gnu gpgv libacl1 libapt-pkg6.0t64 libasan8 libatomic1 libcap-ng0 libcc1-0 libcom-err2 libdebconfclient0 libext2fs2t64 libgcc-14-dev libgcc-s1 libgomp1 libhwasan0 libitm1 liblsan0 liblzma5 libquadmath0 libss2 libssl3t64 libstdc++-14-dev libstdc++6 libsystemd0 libtsan2 libubsan1 libudev1 linux-libc-dev logsave openssl-provider-legacy sysvinit-utils xz-utils 43 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 74.8 MB of archives. After this operation, 102 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 bash amd64 5.2.32-1+b2 [1500 kB] Get:2 http://localhost:3142/debian unstable/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libcc1-0 amd64 14.2.0-7 [42.8 kB] Get:4 http://localhost:3142/debian unstable/main amd64 gcc-14-base amd64 14.2.0-7 [46.9 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libgcc-s1 amd64 14.2.0-7 [72.8 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libgomp1 amd64 14.2.0-7 [137 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libitm1 amd64 14.2.0-7 [26.0 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libatomic1 amd64 14.2.0-7 [9284 B] Get:9 http://localhost:3142/debian unstable/main amd64 libasan8 amd64 14.2.0-7 [2729 kB] Get:10 http://localhost:3142/debian unstable/main amd64 liblsan0 amd64 14.2.0-7 [1205 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libtsan2 amd64 14.2.0-7 [2460 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 14.2.0-7 [1075 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libhwasan0 amd64 14.2.0-7 [1489 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libquadmath0 amd64 14.2.0-7 [145 kB] Get:15 http://localhost:3142/debian unstable/main amd64 gcc-14 amd64 14.2.0-7 [527 kB] Get:16 http://localhost:3142/debian unstable/main amd64 g++-14 amd64 14.2.0-7 [20.0 kB] Get:17 http://localhost:3142/debian unstable/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-7 [12.1 MB] Get:18 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev amd64 14.2.0-7 [2368 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev amd64 14.2.0-7 [2673 kB] Get:20 http://localhost:3142/debian unstable/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-7 [21.4 MB] Get:21 http://localhost:3142/debian unstable/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-7 [11.1 MB] Get:22 http://localhost:3142/debian unstable/main amd64 cpp-14 amd64 14.2.0-7 [1276 B] Get:23 http://localhost:3142/debian unstable/main amd64 libstdc++6 amd64 14.2.0-7 [713 kB] Get:24 http://localhost:3142/debian unstable/main amd64 liblzma5 amd64 5.6.3-1 [272 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libsystemd0 amd64 256.7-2 [382 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libudev1 amd64 256.7-2 [145 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.10 [1045 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libdebconfclient0 amd64 0.272+b1 [10.3 kB] Get:29 http://localhost:3142/debian unstable/main amd64 base-passwd amd64 3.6.5 [53.1 kB] Get:30 http://localhost:3142/debian unstable/main amd64 gpgv amd64 2.2.45-1 [218 kB] Get:31 http://localhost:3142/debian unstable/main amd64 apt amd64 2.9.10 [1413 kB] Get:32 http://localhost:3142/debian unstable/main amd64 sysvinit-utils amd64 3.11-1 [33.1 kB] Get:33 http://localhost:3142/debian unstable/main amd64 logsave amd64 1.47.1-1+b1 [23.0 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libext2fs2t64 amd64 1.47.1-1+b1 [211 kB] Get:35 http://localhost:3142/debian unstable/main amd64 e2fsprogs amd64 1.47.1-1+b1 [585 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libcap-ng0 amd64 0.8.5-3 [17.2 kB] Get:38 http://localhost:3142/debian unstable/main amd64 openssl-provider-legacy amd64 3.3.2-2 [298 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libssl3t64 amd64 3.3.2-2 [2271 kB] Get:40 http://localhost:3142/debian unstable/main amd64 xz-utils amd64 5.6.3-1 [542 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libss2 amd64 1.47.1-1+b1 [27.9 kB] Get:43 http://localhost:3142/debian unstable/main amd64 linux-libc-dev all 6.11.5-1 [2443 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.8 MB in 0s (179 MB/s) (Reading database ... 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Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.1-1+b1) over (1.47.1-1) ... Setting up libext2fs2t64:amd64 (1.47.1-1+b1) ... (Reading database ... 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Unpacking linux-libc-dev (6.11.5-1) over (6.11.2-1) ... Setting up linux-libc-dev (6.11.5-1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up libgomp1:amd64 (14.2.0-7) ... Setting up xz-utils (5.6.3-1) ... Setting up libquadmath0:amd64 (14.2.0-7) ... Setting up libatomic1:amd64 (14.2.0-7) ... Setting up libss2:amd64 (1.47.1-1+b1) ... Setting up cpp-14-x86-64-linux-gnu (14.2.0-7) ... Setting up logsave (1.47.1-1+b1) ... Setting up cpp-14 (14.2.0-7) ... Setting up libubsan1:amd64 (14.2.0-7) ... Setting up libhwasan0:amd64 (14.2.0-7) ... Setting up libasan8:amd64 (14.2.0-7) ... Setting up libtsan2:amd64 (14.2.0-7) ... Setting up libcc1-0:amd64 (14.2.0-7) ... Setting up liblsan0:amd64 (14.2.0-7) ... Setting up libitm1:amd64 (14.2.0-7) ... Setting up e2fsprogs (1.47.1-1+b1) ... Setting up libgcc-14-dev:amd64 (14.2.0-7) ... Setting up libstdc++-14-dev:amd64 (14.2.0-7) ... Setting up gcc-14-x86-64-linux-gnu (14.2.0-7) ... Setting up gcc-14 (14.2.0-7) ... Setting up g++-14-x86-64-linux-gnu (14.2.0-7) ... Setting up g++-14 (14.2.0-7) ... Processing triggers for debianutils (5.20) ... Processing triggers for libc-bin (2.40-3) ... +------------------------------------------------------------------------------+ | 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://localhost:3142/debian unstable/main velvet 1.2.10+dfsg1-9 (dsc) [2393 B] Get:2 http://localhost:3142/debian unstable/main velvet 1.2.10+dfsg1-9 (tar) [13.6 MB] Get:3 http://localhost:3142/debian unstable/main velvet 1.2.10+dfsg1-9 (diff) [18.5 kB] Fetched 13.7 MB in 2s (7583 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/velvet-Nca9HA/velvet-1.2.10+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-Nca9HA' 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:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel 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 [773 B] Get:5 copy:/<>/apt_archive ./ Packages [816 B] Fetched 2198 B in 0s (0 B/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-arm-linux-gnueabi bsdextrautils cpp-14-arm-linux-gnueabi cpp-arm-linux-gnueabi crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern g++-14-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-14-arm-linux-gnueabi gcc-14-arm-linux-gnueabi-base gcc-14-base:armel gcc-14-cross-base-ports gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:armel libasan8-armel-cross libatomic1:armel libatomic1-armel-cross libbrotli1 libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcairo2 libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-14-dev:armel libgcc-14-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0t64 libgomp1:armel libgomp1-armel-cross libgraphite2-3 libharfbuzz0b libice6 libicu72 libkpathsea6 libmagic-mgc libmagic1t64 libmpfi0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libsm6 libstdc++-14-dev:armel libstdc++-14-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsynctex2 libteckit0 libtexlua53-5 libtool libubsan1:armel libubsan1-armel-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-armel-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:armel zlib1g-dev:armel 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-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel libnss-nis:armel libnss-nisplus:armel manpages-dev:armel low-memory-monitor libmpfi-doc libstdc++-14-doc:armel 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:armel 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-arm-linux-gnueabi bsdextrautils cpp-14-arm-linux-gnueabi cpp-arm-linux-gnueabi crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern g++-14-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-14-arm-linux-gnueabi gcc-14-arm-linux-gnueabi-base gcc-14-base:armel gcc-14-cross-base-ports gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:armel libasan8-armel-cross libatomic1:armel libatomic1-armel-cross libbrotli1 libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcairo2 libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-14-dev:armel libgcc-14-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0t64 libgomp1:armel libgomp1-armel-cross libgraphite2-3 libharfbuzz0b libice6 libicu72 libkpathsea6 libmagic-mgc libmagic1t64 libmpfi0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libsm6 libstdc++-14-dev:armel libstdc++-14-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsynctex2 libteckit0 libtexlua53-5 libtool libubsan1:armel libubsan1-armel-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-armel-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:armel sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils zlib1g:armel zlib1g-dev:armel 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 145 MB of archives. After this operation, 506 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B] Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:12 http://localhost:3142/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:13 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:15 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://localhost:3142/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:18 http://localhost:3142/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.43.1-5 [3305 kB] Get:19 http://localhost:3142/debian unstable/main amd64 gcc-14-arm-linux-gnueabi-base amd64 14.2.0-6cross1 [46.9 kB] Get:20 http://localhost:3142/debian unstable/main amd64 cpp-14-arm-linux-gnueabi amd64 14.2.0-6cross1 [10.4 MB] Get:21 http://localhost:3142/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:14.2.0-1 [4132 B] Get:22 http://localhost:3142/debian unstable/main amd64 gcc-14-cross-base-ports all 14.2.0-6cross1 [42.2 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libc6-armel-cross all 2.40-3cross1 [912 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libgcc-s1-armel-cross all 14.2.0-6cross1 [39.0 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libgomp1-armel-cross all 14.2.0-6cross1 [110 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libatomic1-armel-cross all 14.2.0-6cross1 [9256 B] Get:27 http://localhost:3142/debian unstable/main amd64 libasan8-armel-cross all 14.2.0-6cross1 [2536 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libstdc++6-armel-cross all 14.2.0-6cross1 [546 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libubsan1-armel-cross all 14.2.0-6cross1 [1034 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev-armel-cross all 14.2.0-6cross1 [761 kB] Get:31 http://localhost:3142/debian unstable/main amd64 gcc-14-arm-linux-gnueabi amd64 14.2.0-6cross1 [19.8 MB] Get:32 http://localhost:3142/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:14.2.0-1 [1452 B] Get:33 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-armel-cross all 6.11.2-1cross1 [2228 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libc6-dev-armel-cross all 2.40-3cross1 [1326 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev-armel-cross all 14.2.0-6cross1 [2336 kB] Get:36 http://localhost:3142/debian unstable/main amd64 g++-14-arm-linux-gnueabi amd64 14.2.0-6cross1 [11.4 MB] Get:37 http://localhost:3142/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:14.2.0-1 [1204 B] Get:38 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-armel all 12.12 [3552 B] Get:39 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:41 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:44 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:45 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:46 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:49 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:50 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:51 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:52 http://localhost:3142/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:54 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:55 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:56 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:57 http://localhost:3142/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:58 http://localhost:3142/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:59 http://localhost:3142/debian unstable/main armel gcc-14-base armel 14.2.0-7 [46.9 kB] Get:60 http://localhost:3142/debian unstable/main armel libgcc-s1 armel 14.2.0-7 [38.9 kB] Get:61 http://localhost:3142/debian unstable/main armel libc6 armel 2.40-3 [2176 kB] Get:62 http://localhost:3142/debian unstable/main armel libasan8 armel 14.2.0-7 [2549 kB] Get:63 http://localhost:3142/debian unstable/main armel libatomic1 armel 14.2.0-7 [9508 B] Get:64 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get:65 http://localhost:3142/debian unstable/main armel libcrypt1 armel 1:4.4.36-5 [97.0 kB] Get:66 http://localhost:3142/debian unstable/main armel libcrypt-dev armel 1:4.4.36-5 [126 kB] Get:67 http://localhost:3142/debian unstable/main armel libc6-dev armel 2.40-3 [1329 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:83 http://localhost:3142/debian unstable/main armel libgomp1 armel 14.2.0-7 [112 kB] Get:84 http://localhost:3142/debian unstable/main armel libstdc++6 armel 14.2.0-7 [594 kB] Get:85 http://localhost:3142/debian unstable/main armel libubsan1 armel 14.2.0-7 [1035 kB] Get:86 http://localhost:3142/debian unstable/main armel libgcc-14-dev armel 14.2.0-7 [760 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:90 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [157 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:96 http://localhost:3142/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [49.1 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:99 http://localhost:3142/debian unstable/main armel libstdc++-14-dev armel 14.2.0-7 [2370 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [62.5 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [114 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:109 http://localhost:3142/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:110 http://localhost:3142/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get:111 http://localhost:3142/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8493 kB] Get:112 http://localhost:3142/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:113 http://localhost:3142/debian unstable/main amd64 texlive-base all 2024.20240829-2 [22.7 MB] Get:114 http://localhost:3142/debian unstable/main amd64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get:115 http://localhost:3142/debian unstable/main amd64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get:116 http://localhost:3142/debian unstable/main armel zlib1g armel 1:1.3.dfsg+really1.3.1-1 [74.6 kB] Get:117 http://localhost:3142/debian unstable/main armel zlib1g-dev armel 1:1.3.dfsg+really1.3.1-1 [905 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 145 MB in 1s (187 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 13014 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../002-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../005-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Selecting previously unselected package zlib1g:armel. Preparing to unpack .../114-zlib1g_1%3a1.3.dfsg+really1.3.1-1_armel.deb ... Unpacking zlib1g:armel (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package zlib1g-dev:armel. Preparing to unpack .../115-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_armel.deb ... Unpacking zlib1g-dev:armel (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../116-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libexpat1:amd64 (2.6.3-2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up binutils-arm-linux-gnueabi (2.43.1-5) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up gcc-14-base:armel (14.2.0-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b5) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... 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 libxcb-shm0:amd64 (1.17.0-2) ... Setting up file (1:5.45-3+b1) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up linux-libc-dev-armel-cross (6.11.2-1cross1) ... Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up gcc-14-arm-linux-gnueabi-base:amd64 (14.2.0-6cross1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:amd64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Setting up autoconf (2.72-3) ... Setting up libc6-armel-cross (2.40-3cross1) ... Setting up dwz (0.15-1+b1) ... Setting up gcc-14-cross-base-ports (14.2.0-6cross1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libc6-dev-armel-cross (2.40-3cross1) ... Setting up libxml2:amd64 (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:amd64 (2024.20240313.70630+ds-4) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgomp1-armel-cross (14.2.0-6cross1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up cpp-14-arm-linux-gnueabi (14.2.0-6cross1) ... Setting up libgcc-s1-armel-cross (14.2.0-6cross1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libstdc++6-armel-cross (14.2.0-6cross1) ... Setting up libatomic1-armel-cross (14.2.0-6cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up cpp-arm-linux-gnueabi (4:14.2.0-1) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libubsan1-armel-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 libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libasan8-armel-cross (14.2.0-6cross1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libgcc-14-dev-armel-cross (14.2.0-6cross1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up debhelper (13.20) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up gcc-14-arm-linux-gnueabi (14.2.0-6cross1) ... Setting up libstdc++-14-dev-armel-cross (14.2.0-6cross1) ... 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 g++-14-arm-linux-gnueabi (14.2.0-6cross1) ... Setting up gcc-arm-linux-gnueabi (4:14.2.0-1) ... 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 g++-arm-linux-gnueabi (4:14.2.0-1) ... Setting up texlive-latex-base (2024.20240829-2) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Setting up crossbuild-essential-armel (12.12) ... Setting up libgcc-s1:armel (14.2.0-7) ... Setting up libc6:armel (2.40-3) ... Setting up libasan8:armel (14.2.0-7) ... Setting up libstdc++6:armel (14.2.0-7) ... Setting up zlib1g:armel (1:1.3.dfsg+really1.3.1-1) ... Setting up libcrypt1:armel (1:4.4.36-5) ... Setting up libgomp1:armel (14.2.0-7) ... Setting up libatomic1:armel (14.2.0-7) ... Setting up libubsan1:armel (14.2.0-7) ... Setting up libcrypt-dev:armel (1:4.4.36-5) ... Setting up libc6-dev:armel (2.40-3) ... Setting up libgcc-14-dev:armel (14.2.0-7) ... Setting up libstdc++-14-dev:armel (14.2.0-7) ... Setting up zlib1g-dev:armel (1:1.3.dfsg+really1.3.1-1) ... Setting up sbuild-build-depends-main-dummy:armel (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 (armel included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) amd64 (x86_64) 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-armel-cross_14.2.0-6cross1 libstdc++6_14.2.0-7 libstdc++6-armel-cross_14.2.0-6cross1 linux-libc-dev_6.11.5-1 Package versions: apt_2.9.10 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_3.6.5 bash_5.2.32-1+b2 binutils_2.43.1-5 binutils-arm-linux-gnueabi_2.43.1-5 binutils-common_2.43.1-5 binutils-x86-64-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_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-7 cpp-14-arm-linux-gnueabi_14.2.0-6cross1 cpp-14-x86-64-linux-gnu_14.2.0-7 cpp-arm-linux-gnueabi_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-armel_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 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1+b1 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-arm-linux-gnueabi_14.2.0-6cross1 g++-14-x86-64-linux-gnu_14.2.0-7 g++-arm-linux-gnueabi_4:14.2.0-1 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-7 gcc-14-arm-linux-gnueabi_14.2.0-6cross1 gcc-14-arm-linux-gnueabi-base_14.2.0-6cross1 gcc-14-base_14.2.0-7 gcc-14-cross-base-ports_14.2.0-6cross1 gcc-14-x86-64-linux-gnu_14.2.0-7 gcc-arm-linux-gnueabi_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 gpgv_2.2.45-1 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+b1 libapt-pkg6.0t64_2.9.10 libarchive-zip-perl_1.68-1 libasan8_14.2.0-7 libasan8-armel-cross_14.2.0-6cross1 libatomic1_14.2.0-7 libatomic1-armel-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+b5 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-armel-cross_2.40-3cross1 libc6-dev_2.40-3 libc6-dev-armel-cross_2.40-3cross1 libcairo2_1.18.2-2 libcap-ng0_0.8.5-3 libcap2_1:2.66-5 libcc1-0_14.2.0-7 libcom-err2_1.47.1-1+b1 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+b1 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libelf1t64_0.192-4 libexpat1_2.6.3-2 libext2fs2t64_1.47.1-1+b1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libfontconfig1_2.15.0-1.1+b1 libfreetype6_2.13.3+dfsg-1 libgcc-14-dev_14.2.0-7 libgcc-14-dev-armel-cross_14.2.0-6cross1 libgcc-s1_14.2.0-7 libgcc-s1-armel-cross_14.2.0-6cross1 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libglib2.0-0t64_2.82.2-2 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-7 libgomp1-armel-cross_14.2.0-6cross1 libgpg-error0_1.50-4 libgprofng0_2.43.1-5 libgraphite2-3_1.3.14-2+b1 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 libjansson4_2.14-2+b2 libkpathsea6_2024.20240313.70630+ds-4 liblsan0_14.2.0-7 liblz4-1_1.9.4-3 liblzma5_5.6.3-1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 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 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-5 libsm6_2:1.2.3-1+b1 libsmartcols1_2.40.2-9 libss2_1.47.1-1+b1 libssl3t64_3.3.2-2 libstdc++-14-dev_14.2.0-7 libstdc++-14-dev-armel-cross_14.2.0-6cross1 libstdc++6_14.2.0-7 libstdc++6-armel-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-armel-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_6.11.5-1 linux-libc-dev-armel-cross_6.11.2-1cross1 login_1:4.16.0-2+really2.40.2-9 login.defs_1:4.16.0-4 logsave_1.47.1-1+b1 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 mount_2.40.2-9 ncurses-base_6.5-2 ncurses-bin_6.5-2 openssl-provider-legacy_3.3.2-2 passwd_1:4.16.0-4 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_3.11-1 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 tzdata_2024b-3 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_5.6.3-1 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----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmazSnAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrtrw/9Fix53xMaAsOS+/+ayiJu1CQ9ZzQk dTHcW7I9CoaGIcAW5xv2ftijQyIflHZncoSCPtGRFWEGI4hvBEhPxwcdOqMKOxSx Si3IDGXmq+Oreo1spqUwC3/U1yXS71UFAs9znfTBhG0h8BxZ6OS6glj6STyh2NEl dITOOFVzNRr9jrM80v7vydF0dv4LJoWsMdE+aQgNBsxQph60Bsm3+nriKclv5B2U kamA3uqbCUBuxeXoPxMmrXraRhE6VsKqTsp4VVIcKm5OnQ1DLG5iENMYYyQ8yKdK WVki6GereTkzO5Dh5CzJrDDofiXrpepr7O2zGvIEKnmlStp3icEOmb6X6VgddaS6 l8WSlg3QbF/hayDmG/lvUEk4uxuI3ERA08l6riodrJMvKSRBAnH2WnOxqt1ljjLE VXE87J0Ig/q1fgLstSPEoJexWZwy3UR0BfegzRlUbS6rK/CyJyYQB12ABiiLtIwO XGSZcJq7OtywDX44CpsIMgfc/dOzMhqAuIIzAMIEjh53ldczkfUbXlkgxB4Prwpa 0VpNlPUCWjpdnL/zdTIRYyQy69JshmuPlXE+lmqVVOCBb0tWz6OxJaK5aAlGc9yK DYwM5SBTrHRgieDJBgqibjJkX1dLlRZvRLgiGjCknKCeFx7jkKPhNakQrFO4+XU+ yyGx3WwCjhKdt78= =KJVv -----END PGP SIGNATURE----- gpgv: Signature made Wed Aug 7 10:20:32 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-9.dsc: no acceptable signature found dpkg-source: info: extracting velvet in /<> 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.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.tvD8qnyogL/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-1ba71eb3-cf2a-4f6e-af79-200b8bfd819f SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmel -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 arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel 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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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. 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Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 615. [14] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 642. Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 683 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 695. 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[16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 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="-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc color OPENMP=1 "CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘velvetifySequence’: src/readSet.c:247:17: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 247 | case EOF: | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function ‘fillUpConnectedGraph’: src/graphReConstruction.c:1407:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1407:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1407 | velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld src/graphReConstruction.c:1436:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘__time64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~^ ~~~~~~~~~~~ | | | | long int __time64_t {aka long long int} | %lld src/graphReConstruction.c:1436:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘__suseconds64_t’ {aka ‘long long int’} [-Wformat=] 1436 | velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); | ~~~~^ ~~~~~~~~~~~~ | | | | long int __suseconds64_t {aka long long int} | %06lld In file included from src/graphReConstruction.c:33: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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; | ^~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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]); | ^~~~~~~~~~~ arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 arm-linux-gnueabi-gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux.so.3.usr-is-merged dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-9_armel.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-9_armel.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-9_armel.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-9_armel.deb'. dpkg-genbuildinfo --build=any -O../velvet_1.2.10+dfsg1-9_armel.buildinfo dpkg-genchanges --build=any -O../velvet_1.2.10+dfsg1-9_armel.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 2024-10-29T10:23:41Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ velvet_1.2.10+dfsg1-9_armel.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: armel 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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velvet_1.2.10+dfsg1-9_armel.deb Files: 4ba658a618240980c1d85d6c8f5bb05b 939076 debug optional velvet-dbgsym_1.2.10+dfsg1-9_armel.deb 877ddc8dd52a9394b3e43151b725fafc 2081460 debug optional velvet-long-dbgsym_1.2.10+dfsg1-9_armel.deb 25af38e22e34c77d5644b0518c56efa4 226420 science optional velvet-long_1.2.10+dfsg1-9_armel.deb 6315c01e956dea5c6a76b1a2a2e7c1a7 7071 science optional velvet_1.2.10+dfsg1-9_armel.buildinfo 9472ac8a40fbe1cbefb263605bb2a02c 657980 science optional velvet_1.2.10+dfsg1-9_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Architecture: armel Version: 1.2.10+dfsg1-9 Checksums-Md5: 4ba658a618240980c1d85d6c8f5bb05b 939076 velvet-dbgsym_1.2.10+dfsg1-9_armel.deb 877ddc8dd52a9394b3e43151b725fafc 2081460 velvet-long-dbgsym_1.2.10+dfsg1-9_armel.deb 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Build-Architecture: amd64 Build-Date: Tue, 29 Oct 2024 10:23:41 +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 (= 3.6.5), bash (= 5.2.32-1+b2), binutils (= 2.43.1-5), binutils-common (= 2.43.1-5), binutils-x86-64-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 (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-7), cpp-14-x86-64-linux-gnu (= 14.2.0-7), cpp-x86-64-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+b1), findutils (= 4.10.0-3), fontconfig-config (= 2.15.0-1.1+b1), 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-x86-64-linux-gnu (= 14.2.0-7), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-7), gcc-14-base (= 14.2.0-7), gcc-14-x86-64-linux-gnu (= 14.2.0-7), gcc-x86-64-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+b1), 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+b5), 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 (= 0.8.5-3), 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+b1), libdebhelper-perl (= 13.20), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.192-4), libexpat1 (= 2.6.3-2), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfontconfig1 (= 2.15.0-1.1+b1), 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 (= 2.82.2-2), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-7), libgprofng0 (= 2.43.1-5), libgraphite2-3 (= 1.3.14-2+b1), 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 (= 5.6.3-1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), 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), libquadmath0 (= 14.2.0-7), 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 (= 3.3.2-2), 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 (= 6.11.5-1), 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 (= 3.3.2-2), 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 (= 3.11-1), 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 (= 5.6.3-1), 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_armel.deb -------------------------------------- new Debian package, version 2.0. size 939076 bytes: control archive=748 bytes. 504 bytes, 12 lines control 508 bytes, 5 lines md5sums Package: velvet-dbgsym Source: velvet Version: 1.2.10+dfsg1-9 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 1056 Depends: velvet (= 1.2.10+dfsg1-9) Section: debug Priority: optional Description: debug symbols for velvet Build-Ids: 21158fe02de198a38245dfb741a1aa4be751a871 545e9dbc66bc4a5e31a878628363d060a8035eb8 e9b431e962ca6452823585cc0afae829c3299948 f9e1ca6257f3cb23dc5161e4f43e09137bed6cc7 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/21/ -rw-r--r-- root/root 402140 2024-08-07 09:51 ./usr/lib/debug/.build-id/21/158fe02de198a38245dfb741a1aa4be751a871.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/54/ -rw-r--r-- root/root 106804 2024-08-07 09:51 ./usr/lib/debug/.build-id/54/5e9dbc66bc4a5e31a878628363d060a8035eb8.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/e9/ -rw-r--r-- root/root 401980 2024-08-07 09:51 ./usr/lib/debug/.build-id/e9/b431e962ca6452823585cc0afae829c3299948.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/f9/ -rw-r--r-- root/root 109488 2024-08-07 09:51 ./usr/lib/debug/.build-id/f9/e1ca6257f3cb23dc5161e4f43e09137bed6cc7.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/arm-linux-gnueabi/ -rw-r--r-- root/root 43368 2024-08-07 09:51 ./usr/lib/debug/.dwz/arm-linux-gnueabi/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_armel.deb ------------------------------------------- new Debian package, version 2.0. size 2081460 bytes: control archive=1052 bytes. 765 bytes, 12 lines control 1149 bytes, 11 lines md5sums Package: velvet-long-dbgsym Source: velvet Version: 1.2.10+dfsg1-9 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 2553 Depends: velvet-long (= 1.2.10+dfsg1-9) Section: debug Priority: optional Description: debug symbols for velvet-long Build-Ids: 09ac17d4b29805d5bdd82659424395dfd41e0a4f 0d1a8fe51b88fd6b20eb736d22a366b141db5070 2aff032ef5dc558b57b3d4f45fb30d7786adf4b9 34eb852a87be5213ed0e49bbc51b87030fdd6f87 57aac7fedbf585b943b58527e122fc811e2fcf22 6402647c284b8fd576c33906425959ad3491336b c0cd5c2c43b9ccad354f3b53c86a0302377c236a c6b8f12ea664188b3e431cf4f8a9ca67aa83f937 cf6407abf4b0625fb56b66d6bcbe49fe116f62fe de07803090f7714ec594b11eb7a4675af6517848 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/09/ -rw-r--r-- root/root 401332 2024-08-07 09:51 ./usr/lib/debug/.build-id/09/ac17d4b29805d5bdd82659424395dfd41e0a4f.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/0d/ -rw-r--r-- root/root 106752 2024-08-07 09:51 ./usr/lib/debug/.build-id/0d/1a8fe51b88fd6b20eb736d22a366b141db5070.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/2a/ -rw-r--r-- root/root 106716 2024-08-07 09:51 ./usr/lib/debug/.build-id/2a/ff032ef5dc558b57b3d4f45fb30d7786adf4b9.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/34/ -rw-r--r-- root/root 401832 2024-08-07 09:51 ./usr/lib/debug/.build-id/34/eb852a87be5213ed0e49bbc51b87030fdd6f87.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/57/ -rw-r--r-- root/root 106856 2024-08-07 09:51 ./usr/lib/debug/.build-id/57/aac7fedbf585b943b58527e122fc811e2fcf22.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/64/ -rw-r--r-- root/root 106888 2024-08-07 09:51 ./usr/lib/debug/.build-id/64/02647c284b8fd576c33906425959ad3491336b.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/c0/ -rw-r--r-- root/root 107060 2024-08-07 09:51 ./usr/lib/debug/.build-id/c0/cd5c2c43b9ccad354f3b53c86a0302377c236a.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/c6/ -rw-r--r-- root/root 401756 2024-08-07 09:51 ./usr/lib/debug/.build-id/c6/b8f12ea664188b3e431cf4f8a9ca67aa83f937.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/cf/ -rw-r--r-- root/root 401656 2024-08-07 09:51 ./usr/lib/debug/.build-id/cf/6407abf4b0625fb56b66d6bcbe49fe116f62fe.debug drwxr-xr-x root/root 0 2024-08-07 09:51 ./usr/lib/debug/.build-id/de/ -rw-r--r-- root/root 401188 2024-08-07 09:51 ./usr/lib/debug/.build-id/de/07803090f7714ec594b11eb7a4675af6517848.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/arm-linux-gnueabi/ -rw-r--r-- root/root 45044 2024-08-07 09:51 ./usr/lib/debug/.dwz/arm-linux-gnueabi/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_armel.deb ------------------------------------ new Debian package, version 2.0. size 226420 bytes: control archive=1456 bytes. 999 bytes, 22 lines control 1499 bytes, 23 lines md5sums Package: velvet-long Source: velvet Version: 1.2.10+dfsg1-9 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 2126 Depends: libc6 (>= 2.34), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.3.4), 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 329880 2024-08-07 09:51 ./usr/bin/velvetg_127 -rwxr-xr-x root/root 329880 2024-08-07 09:51 ./usr/bin/velvetg_127_long -rwxr-xr-x root/root 329880 2024-08-07 09:51 ./usr/bin/velvetg_63 -rwxr-xr-x root/root 329880 2024-08-07 09:51 ./usr/bin/velvetg_63_long -rwxr-xr-x root/root 329868 2024-08-07 09:51 ./usr/bin/velvetg_long -rwxr-xr-x root/root 96328 2024-08-07 09:51 ./usr/bin/velveth_127 -rwxr-xr-x root/root 96328 2024-08-07 09:51 ./usr/bin/velveth_127_long -rwxr-xr-x root/root 96328 2024-08-07 09:51 ./usr/bin/velveth_63 -rwxr-xr-x root/root 96328 2024-08-07 09:51 ./usr/bin/velveth_63_long -rwxr-xr-x root/root 92220 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_armel.deb ------------------------------- new Debian package, version 2.0. size 657980 bytes: control archive=1324 bytes. 877 bytes, 19 lines control 1161 bytes, 18 lines md5sums Package: velvet Version: 1.2.10+dfsg1-9 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 1381 Depends: libc6 (>= 2.34), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.3.4) 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 325768 2024-08-07 09:51 ./usr/bin/velvetg -rwxr-xr-x root/root 325768 2024-08-07 09:51 ./usr/bin/velvetg_de -rwxr-xr-x root/root 96312 2024-08-07 09:51 ./usr/bin/velveth -rwxr-xr-x root/root 96312 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:amd64 Filtered Build-Depends: lintian:amd64 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 [1355 B] Get:5 copy:/<>/apt_archive ./ Packages [1434 B] Fetched 3404 B in 0s (0 B/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 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 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:armel shared-mime-info unzip 0 upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 16.9 MB of archives. After this operation, 69.3 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get:4 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:5 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:6 http://localhost:3142/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:10 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:20 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libstemmer0d amd64 2.2.0-4+b1 [119 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libxmlb2 amd64 0.3.21-1 [63.0 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libappstream5 amd64 1.0.3-1+b1 [224 kB] Get:27 http://localhost:3142/debian unstable/main amd64 appstream amd64 1.0.3-1+b1 [469 kB] Get:28 http://localhost:3142/debian unstable/main amd64 diffstat amd64 1.66-1 [34.0 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:31 http://localhost:3142/debian unstable/main amd64 gpgconf amd64 2.2.45-1 [120 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:33 http://localhost:3142/debian unstable/main amd64 gpg amd64 2.2.45-1 [531 kB] Get:34 http://localhost:3142/debian unstable/main amd64 iso-codes all 4.17.0-1 [3055 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.40+b6 [67.8 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:45 http://localhost:3142/debian unstable/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libberkeleydb-perl amd64 0.66-1 [121 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:50 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b1 [99.7 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libcgi-pm-perl all 4.66-1 [217 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:54 http://localhost:3142/debian unstable/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:64 http://localhost:3142/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libdata-dpath-perl all 0.60-1 [41.8 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libdata-messagepack-perl amd64 1.02-1+b4 [32.8 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-4 [31.5 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libdata-validate-domain-perl all 0.15-1 [11.9 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b4 [98.1 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libdevel-size-perl amd64 0.84-1+b1 [24.2 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libemail-address-xs-perl amd64 1.05-1+b4 [29.4 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:84 http://localhost:3142/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:85 http://localhost:3142/debian unstable/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:93 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libhtml-form-perl all 6.12-1 [32.3 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:100 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:101 http://localhost:3142/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:104 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:112 http://localhost:3142/debian unstable/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:113 http://localhost:3142/debian unstable/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:114 http://localhost:3142/debian unstable/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:115 http://localhost:3142/debian unstable/main amd64 liblz1 amd64 1.15~pre2-1 [39.2 kB] Get:116 http://localhost:3142/debian unstable/main amd64 liblzo2-2 amd64 2.10-3 [54.4 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2+b1 [35.6 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:119 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:124 http://localhost:3142/debian unstable/main amd64 libmouse-perl amd64 2.5.11-1+b1 [144 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libsub-name-perl amd64 0.27-1+b3 [12.5 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:129 http://localhost:3142/debian unstable/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get:130 http://localhost:3142/debian unstable/main amd64 libperlio-gzip-perl amd64 0.20-1+b4 [17.5 kB] Get:131 http://localhost:3142/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get:132 http://localhost:3142/debian unstable/main amd64 libproc-processtable-perl amd64 0.636-1+b3 [42.3 kB] Get:133 http://localhost:3142/debian unstable/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:134 http://localhost:3142/debian unstable/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b3 [100 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b3 [104 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:137 http://localhost:3142/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.46-1+b1 [64.9 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.30-1+b1 [27.4 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get:140 http://localhost:3142/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b4 [8720 B] Get:141 http://localhost:3142/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.16-1+b3 [13.0 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-2+b1 [174 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libtime-moment-perl amd64 0.44-2+b4 [73.2 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-2+b3 [20.4 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libwww-mechanize-perl all 2.19-1 [114 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:149 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:150 http://localhost:3142/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5+b1 [314 kB] Get:151 http://localhost:3142/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.902.0+ds-2+b1 [35.5 kB] Get:152 http://localhost:3142/debian unstable/main amd64 plzip amd64 1.11-2 [63.6 kB] Get:153 http://localhost:3142/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:154 http://localhost:3142/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:155 http://localhost:3142/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get:156 http://localhost:3142/debian unstable/main amd64 lintian all 2.119.0 [1056 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.9 MB in 0s (155 MB/s) Selecting previously unselected package netbase. (Reading database ... 27287 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../004-shared-mime-info_2.4-5+b1_amd64.deb ... Unpacking shared-mime-info (2.4-5+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../005-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../006-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../007-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../008-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../009-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../010-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../011-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../012-libldap-2.5-0_2.5.18+dfsg-3+b1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../013-libnghttp2-14_1.63.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.63.0-1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../014-libnghttp3-9_1.4.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../015-libngtcp2-16_1.6.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../016-libngtcp2-crypto-gnutls8_1.6.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../017-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../018-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../019-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../020-libcurl3t64-gnutls_8.10.1-2_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.10.1-2) ... Selecting previously unselected package libstemmer0d:amd64. Preparing to unpack .../021-libstemmer0d_2.2.0-4+b1_amd64.deb ... Unpacking libstemmer0d:amd64 (2.2.0-4+b1) ... Selecting previously unselected package libxmlb2:amd64. Preparing to unpack .../022-libxmlb2_0.3.21-1_amd64.deb ... Unpacking libxmlb2:amd64 (0.3.21-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../023-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package libappstream5:amd64. Preparing to unpack .../024-libappstream5_1.0.3-1+b1_amd64.deb ... Unpacking libappstream5:amd64 (1.0.3-1+b1) ... Selecting previously unselected package appstream. Preparing to unpack .../025-appstream_1.0.3-1+b1_amd64.deb ... Unpacking appstream (1.0.3-1+b1) ... Selecting previously unselected package diffstat. Preparing to unpack .../026-diffstat_1.66-1_amd64.deb ... Unpacking diffstat (1.66-1) ... Selecting previously unselected package libassuan9:amd64. Preparing to unpack .../027-libassuan9_3.0.1-2_amd64.deb ... Unpacking libassuan9:amd64 (3.0.1-2) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../028-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../029-gpgconf_2.2.45-1_amd64.deb ... Unpacking gpgconf (2.2.45-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../030-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package gpg. 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Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../037-libdevel-callchecker-perl_0.009-1+b1_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../038-libparams-classify-perl_0.015-2+b4_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b4) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../039-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../040-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../041-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... 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Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../063-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../064-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../065-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../066-libiterator-util-perl_0.02+ds1-2_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-2) ... Selecting previously unselected package libdata-dpath-perl. Preparing to unpack .../067-libdata-dpath-perl_0.60-1_all.deb ... Unpacking libdata-dpath-perl (0.60-1) ... Selecting previously unselected package libdata-messagepack-perl. 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Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../079-libipc-system-simple-perl_1.30-2_all.deb ... Unpacking libipc-system-simple-perl (1.30-2) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../080-libfile-basedir-perl_0.09-2_all.deb ... Unpacking libfile-basedir-perl (0.09-2) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../081-libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../082-libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../083-libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package libtimedate-perl. 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Selecting previously unselected package liblist-utilsby-perl. Preparing to unpack .../112-liblist-utilsby-perl_0.12-2_all.deb ... Unpacking liblist-utilsby-perl (0.12-2) ... Selecting previously unselected package liblz1:amd64. Preparing to unpack .../113-liblz1_1.15~pre2-1_amd64.deb ... Unpacking liblz1:amd64 (1.15~pre2-1) ... Selecting previously unselected package liblzo2-2:amd64. Preparing to unpack .../114-liblzo2-2_2.10-3_amd64.deb ... Unpacking liblzo2-2:amd64 (2.10-3) ... Selecting previously unselected package libmarkdown2:amd64. Preparing to unpack .../115-libmarkdown2_2.2.7-2+b1_amd64.deb ... Unpacking libmarkdown2:amd64 (2.2.7-2+b1) ... Selecting previously unselected package libmldbm-perl. Preparing to unpack .../116-libmldbm-perl_2.05-4_all.deb ... Unpacking libmldbm-perl (2.05-4) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../117-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... 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Unpacking libpackage-stash-perl (0.40-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../124-libsub-identify-perl_0.14-3+b3_amd64.deb ... Unpacking libsub-identify-perl (0.14-3+b3) ... Selecting previously unselected package libsub-name-perl:amd64. Preparing to unpack .../125-libsub-name-perl_0.27-1+b3_amd64.deb ... Unpacking libsub-name-perl:amd64 (0.27-1+b3) ... Selecting previously unselected package libnamespace-clean-perl. Preparing to unpack .../126-libnamespace-clean-perl_0.27-2_all.deb ... Unpacking libnamespace-clean-perl (0.27-2) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../127-libpath-tiny-perl_0.146-1_all.deb ... Unpacking libpath-tiny-perl (0.146-1) ... Selecting previously unselected package libperlio-gzip-perl. Preparing to unpack .../128-libperlio-gzip-perl_0.20-1+b4_amd64.deb ... Unpacking libperlio-gzip-perl (0.20-1+b4) ... Selecting previously unselected package libperlio-utf8-strict-perl. Preparing to unpack .../129-libperlio-utf8-strict-perl_0.010-1+b3_amd64.deb ... Unpacking libperlio-utf8-strict-perl (0.010-1+b3) ... Selecting previously unselected package libproc-processtable-perl:amd64. Preparing to unpack .../130-libproc-processtable-perl_0.636-1+b3_amd64.deb ... Unpacking libproc-processtable-perl:amd64 (0.636-1+b3) ... Selecting previously unselected package libregexp-wildcards-perl. Preparing to unpack .../131-libregexp-wildcards-perl_1.05-3_all.deb ... Unpacking libregexp-wildcards-perl (1.05-3) ... Selecting previously unselected package libsereal-decoder-perl. Preparing to unpack .../132-libsereal-decoder-perl_5.004+ds-1+b3_amd64.deb ... Unpacking libsereal-decoder-perl (5.004+ds-1+b3) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../133-libsereal-encoder-perl_5.004+ds-1+b3_amd64.deb ... Unpacking libsereal-encoder-perl (5.004+ds-1+b3) ... 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Unpacking sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b6) ... Setting up liblz1:amd64 (1.15~pre2-1) ... Setting up libberkeleydb-perl:amd64 (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:amd64 (1.6.3-4) ... Setting up libunicode-utf8-perl (0.62-2+b3) ... Setting up libmouse-perl:amd64 (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:amd64 (0.47-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up libsub-identify-perl (0.14-3+b3) ... Setting up libcpanel-json-xs-perl:amd64 (4.38-1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxmlb2:amd64 (0.3.21-1) ... Setting up libdevel-size-perl (0.84-1+b1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:amd64 (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:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up liblzo2-2:amd64 (2.10-3) ... Setting up libtime-moment-perl (0.44-2+b4) ... Setting up libencode-locale-perl (1.05-3) ... 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:amd64 (1.21.3-3) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:amd64 (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 (0.10-1) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up librtmp1:amd64 (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:amd64 (0.22-3+b2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-2+b1) ... Setting up libnghttp3-9:amd64 (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:amd64 (0.27-1+b3) ... Setting up libdata-validate-domain-perl (0.15-1) ... Setting up libproc-processtable-perl:amd64 (0.636-1+b3) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up lzop (1.04-2) ... Setting up libassuan9:amd64 (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:amd64 (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:amd64 (1.21.3-3) ... Setting up libstemmer0d:amd64 (2.2.0-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.3.2-2) ... 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:amd64 (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:amd64 (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:amd64 (1.94-2) ... 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:amd64 (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:amd64 (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:amd64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libreadline8t64:amd64 (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:amd64 (3.83-1+b1) ... Setting up gpgconf (2.2.45-1) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.45-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhtml-form-perl (6.12-1) ... 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:amd64 (0.015-2+b4) ... Setting up libcgi-pm-perl (4.66-1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up libappstream5:amd64 (1.0.3-1+b1) ... Setting up appstream (1.0.3-1+b1) ... ✔ 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:armel (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: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 81032 Build-Time: 96 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 41 Job: velvet_1.2.10+dfsg1-9 Lintian: pass Machine Architecture: amd64 Package: velvet Package-Time: 155 Source-Version: 1.2.10+dfsg1-9 Space: 81032 Status: successful Version: 1.2.10+dfsg1-9 -------------------------------------------------------------------------------- Finished at 2024-10-29T10:23:41Z Build needed 00:02:35, 81032k disk space