sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | velvet 1.2.10+dfsg1-8 (armhf) Fri, 10 Nov 2023 23:05:15 +0000 | +==============================================================================+ Package: velvet Version: 1.2.10+dfsg1-8 Source Version: 1.2.10+dfsg1-8 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-63d8ee55-69bc-4adc-a643-6814e78a9723' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-S4FsoV/resolver-Fj3zmX' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://localhost:3142/debian sid InRelease Get:2 http://localhost:3142/debian sid/main armhf Packages [9154 kB] Fetched 9154 kB in 1s (8726 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.6 MB of source archives. Get:1 http://localhost:3142/debian sid/main velvet 1.2.10+dfsg1-8 (dsc) [2270 B] Get:2 http://localhost:3142/debian sid/main velvet 1.2.10+dfsg1-8 (tar) [13.6 MB] Get:3 http://localhost:3142/debian sid/main velvet 1.2.10+dfsg1-8 (diff) [17.2 kB] Fetched 13.6 MB in 2s (7166 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/velvet-S4FsoV/velvet-1.2.10+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-S4FsoV' 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-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf 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-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf 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-gnueabihf bsdextrautils cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-11-base:armhf gcc-13-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf-base gcc-13-base:armhf gcc-13-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbrotli1 libbsd0 libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcairo2 libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfreetype6 libgcc-11-dev:armhf libgcc-13-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libgraphite2-3 libgssapi-krb5-2:armhf libharfbuzz0b libice6 libicu72 libio-string-perl libk5crypto3:armhf libkeyutils1:armhf libkpathsea6 libkrb5-3:armhf libkrb5support0:armhf liblocale-gettext-perl libmagic-mgc libmagic1 libnsl-dev:armhf libnsl2:armhf libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libptexenc1 libsm6 libssl3:armhf libstdc++-11-dev:armhf libstdc++-13-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxmu6 libxpm4 libxrender1 libxt6 libyaml-perl libzzip-0-13 linux-libc-dev:armhf linux-libc-dev-armhf-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:armhf zlib1g-dev:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf libnss-nis:armhf libnss-nisplus:armhf manpages-dev:armhf low-memory-monitor krb5-doc:armhf krb5-user:armhf libstdc++-11-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl 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:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales:armhf libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl 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-gnueabihf bsdextrautils cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-11-base:armhf gcc-13-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf-base gcc-13-base:armhf gcc-13-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbrotli1 libbsd0 libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcairo2 libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfreetype6 libgcc-11-dev:armhf libgcc-13-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libgraphite2-3 libgssapi-krb5-2:armhf libharfbuzz0b libice6 libicu72 libio-string-perl libk5crypto3:armhf libkeyutils1:armhf libkpathsea6 libkrb5-3:armhf libkrb5support0:armhf liblocale-gettext-perl libmagic-mgc libmagic1 libnsl-dev:armhf libnsl2:armhf libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libptexenc1 libsm6 libssl3:armhf libstdc++-11-dev:armhf libstdc++-13-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxmu6 libxpm4 libxrender1 libxt6 libyaml-perl libzzip-0-13 linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:armhf sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 144 newly installed, 0 to remove and 0 not upgraded. Need to get 144 MB of archives. After this operation, 490 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [948 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6 [15.3 kB] Get:3 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:4 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2 [314 kB] Get:5 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2 [105 kB] Get:6 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2 [42.8 kB] Get:7 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-13+b1 [161 kB] Get:8 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:9 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get:10 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.2-5 [89.1 kB] Get:11 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:12 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-1 [1402 kB] Get:13 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:14 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:15 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:16 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-13 [496 kB] Get:19 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabihf amd64 2.41-6 [3239 kB] Get:20 http://localhost:3142/debian sid/main amd64 gcc-13-arm-linux-gnueabihf-base amd64 13.2.0-6cross1 [40.8 kB] Get:21 http://localhost:3142/debian sid/main amd64 cpp-13-arm-linux-gnueabihf amd64 13.2.0-6cross1 [9284 kB] Get:22 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabihf amd64 4:13.2.0-1 [4124 B] Get:23 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:24 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-6cross1 [36.3 kB] Get:25 http://localhost:3142/debian sid/main amd64 libc6-armhf-cross all 2.37-12cross1 [868 kB] Get:26 http://localhost:3142/debian sid/main amd64 libgcc-s1-armhf-cross all 13.2.0-6cross1 [36.5 kB] Get:27 http://localhost:3142/debian sid/main amd64 libgomp1-armhf-cross all 13.2.0-6cross1 [103 kB] Get:28 http://localhost:3142/debian sid/main amd64 libatomic1-armhf-cross all 13.2.0-6cross1 [6748 B] Get:29 http://localhost:3142/debian sid/main amd64 libasan8-armhf-cross all 13.2.0-6cross1 [2411 kB] Get:30 http://localhost:3142/debian sid/main amd64 libstdc++6-armhf-cross all 13.2.0-6cross1 [545 kB] Get:31 http://localhost:3142/debian sid/main amd64 libubsan1-armhf-cross all 13.2.0-6cross1 [967 kB] Get:32 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-armhf-cross all 13.2.0-6cross1 [781 kB] Get:33 http://localhost:3142/debian sid/main amd64 gcc-13-arm-linux-gnueabihf amd64 13.2.0-6cross1 [18.2 MB] Get:34 http://localhost:3142/debian sid/main amd64 gcc-arm-linux-gnueabihf amd64 4:13.2.0-1 [1476 B] Get:35 http://localhost:3142/debian sid/main amd64 linux-libc-dev-armhf-cross all 6.5.8-1cross1 [1975 kB] Get:36 http://localhost:3142/debian sid/main amd64 libc6-dev-armhf-cross all 2.37-12cross1 [1265 kB] Get:37 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-armhf-cross all 13.2.0-6cross1 [2210 kB] Get:38 http://localhost:3142/debian sid/main amd64 g++-13-arm-linux-gnueabihf amd64 13.2.0-6cross1 [10.2 MB] Get:39 http://localhost:3142/debian sid/main amd64 g++-arm-linux-gnueabihf amd64 4:13.2.0-1 [1180 B] Get:40 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:41 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:42 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:43 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [686 kB] Get:44 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:45 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:46 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:47 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:48 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:49 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:50 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:51 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:52 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:54 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:55 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armhf all 12.10 [3484 B] Get:56 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.7 [82.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:58 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:60 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:61 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:62 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:63 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.189-4 [174 kB] Get:64 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:65 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-13+b1 [1301 kB] Get:66 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:67 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:68 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.7 [956 kB] Get:69 http://localhost:3142/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:70 http://localhost:3142/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:71 http://localhost:3142/debian sid/main amd64 fontconfig-config amd64 2.14.2-6 [316 kB] Get:72 http://localhost:3142/debian sid/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:73 http://localhost:3142/debian sid/main armhf gcc-11-base armhf 11.4.0-5 [40.1 kB] Get:74 http://localhost:3142/debian sid/main armhf gcc-13-base armhf 13.2.0-6 [40.5 kB] Get:75 http://localhost:3142/debian sid/main armhf libgcc-s1 armhf 13.2.0-6 [36.6 kB] Get:76 http://localhost:3142/debian sid/main armhf libc6 armhf 2.37-12 [2131 kB] Get:77 http://localhost:3142/debian sid/main armhf libasan6 armhf 11.4.0-5 [1971 kB] Get:78 http://localhost:3142/debian sid/main armhf libatomic1 armhf 13.2.0-6 [7004 B] Get:79 http://localhost:3142/debian sid/main amd64 libbrotli1 amd64 1.1.0-1 [299 kB] Get:80 http://localhost:3142/debian sid/main amd64 libbsd0 amd64 0.11.7-4 [115 kB] Get:81 http://localhost:3142/debian sid/main armhf linux-libc-dev armhf 6.5.10-1 [1977 kB] Get:82 http://localhost:3142/debian sid/main armhf libcrypt1 armhf 1:4.4.36-2 [95.7 kB] Get:83 http://localhost:3142/debian sid/main armhf libcrypt-dev armhf 1:4.4.36-2 [125 kB] Get:84 http://localhost:3142/debian sid/main armhf libkrb5support0 armhf 1.20.1-5 [30.0 kB] Get:85 http://localhost:3142/debian sid/main armhf libcom-err2 armhf 1.47.0-2+b1 [19.3 kB] Get:86 http://localhost:3142/debian sid/main armhf libk5crypto3 armhf 1.20.1-5 [74.8 kB] Get:87 http://localhost:3142/debian sid/main armhf libkeyutils1 armhf 1.6.3-2 [7832 B] Get:88 http://localhost:3142/debian sid/main armhf libssl3 armhf 3.0.12-2 [1672 kB] Get:89 http://localhost:3142/debian sid/main armhf libkrb5-3 armhf 1.20.1-5 [287 kB] Get:90 http://localhost:3142/debian sid/main armhf libgssapi-krb5-2 armhf 1.20.1-5 [111 kB] Get:91 http://localhost:3142/debian sid/main armhf libtirpc3 armhf 1.3.3+ds-1 [72.9 kB] Get:92 http://localhost:3142/debian sid/main armhf libnsl2 armhf 1.3.0-3 [33.7 kB] Get:93 http://localhost:3142/debian sid/main armhf libtirpc-dev armhf 1.3.3+ds-1 [182 kB] Get:94 http://localhost:3142/debian sid/main armhf libnsl-dev armhf 1.3.0-3 [61.8 kB] Get:95 http://localhost:3142/debian sid/main armhf libc6-dev armhf 2.37-12 [1267 kB] Get:96 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:97 http://localhost:3142/debian sid/main amd64 libpng16-16 amd64 1.6.40-2 [276 kB] Get:98 http://localhost:3142/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1 [437 kB] Get:99 http://localhost:3142/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6 [387 kB] Get:100 http://localhost:3142/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:101 http://localhost:3142/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:102 http://localhost:3142/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:103 http://localhost:3142/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:104 http://localhost:3142/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:105 http://localhost:3142/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:106 http://localhost:3142/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:107 http://localhost:3142/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:108 http://localhost:3142/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:109 http://localhost:3142/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:110 http://localhost:3142/debian sid/main amd64 libcairo2 amd64 1.18.0-1 [530 kB] Get:111 http://localhost:3142/debian sid/main armhf libgomp1 armhf 13.2.0-6 [105 kB] Get:112 http://localhost:3142/debian sid/main armhf libstdc++6 armhf 13.2.0-6 [592 kB] Get:113 http://localhost:3142/debian sid/main armhf libubsan1 armhf 13.2.0-6 [968 kB] Get:114 http://localhost:3142/debian sid/main armhf libgcc-11-dev armhf 11.4.0-5 [708 kB] Get:115 http://localhost:3142/debian sid/main amd64 libglib2.0-0 amd64 2.78.1-3 [1451 kB] Get:116 http://localhost:3142/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:117 http://localhost:3142/debian sid/main amd64 libharfbuzz0b amd64 8.0.1-1 [2158 kB] Get:118 http://localhost:3142/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:119 http://localhost:3142/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:120 http://localhost:3142/debian sid/main amd64 libkpathsea6 amd64 2023.20230311.66589-7 [154 kB] Get:121 http://localhost:3142/debian sid/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:122 http://localhost:3142/debian sid/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:123 http://localhost:3142/debian sid/main amd64 libpotrace0 amd64 1.16-2 [26.2 kB] Get:124 http://localhost:3142/debian sid/main amd64 libptexenc1 amd64 2023.20230311.66589-7 [46.7 kB] Get:125 http://localhost:3142/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:126 http://localhost:3142/debian sid/main armhf libstdc++-11-dev armhf 11.4.0-5 [1995 kB] Get:127 http://localhost:3142/debian sid/main amd64 libsynctex2 amd64 2023.20230311.66589-7 [61.7 kB] Get:128 http://localhost:3142/debian sid/main amd64 libteckit0 amd64 2.5.11+ds1-1+b1 [335 kB] Get:129 http://localhost:3142/debian sid/main amd64 libtexlua53-5 amd64 2023.20230311.66589-7 [113 kB] Get:130 http://localhost:3142/debian sid/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:131 http://localhost:3142/debian sid/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get:132 http://localhost:3142/debian sid/main amd64 libxpm4 amd64 1:3.5.17-1 [55.8 kB] Get:133 http://localhost:3142/debian sid/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB] Get:134 http://localhost:3142/debian sid/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:135 http://localhost:3142/debian sid/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB] Get:136 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:137 http://localhost:3142/debian sid/main amd64 tex-common all 6.18 [32.5 kB] Get:138 http://localhost:3142/debian sid/main amd64 texlive-binaries amd64 2023.20230311.66589-7 [8472 kB] Get:139 http://localhost:3142/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:140 http://localhost:3142/debian sid/main amd64 texlive-base all 2023.20231007-1 [22.0 MB] Get:141 http://localhost:3142/debian sid/main amd64 texlive-latex-base all 2023.20231007-1 [1239 kB] Get:142 http://localhost:3142/debian sid/main amd64 texlive-latex-recommended all 2023.20231007-1 [8835 kB] Get:143 http://localhost:3142/debian sid/main armhf zlib1g armhf 1:1.2.13.dfsg-3 [73.8 kB] Get:144 http://localhost:3142/debian sid/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [902 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 144 MB in 1s (189 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14615 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-6_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-2_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.45-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-2_amd64.deb ... Unpacking file (1:5.45-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-13+b1_amd64.deb ... Unpacking gettext-base (0.21-13+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-3_amd64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.39.2-5_amd64.deb ... Unpacking bsdextrautils (2.39.2-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.12.0-1_amd64.deb ... Unpacking man-db (2.12.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../011-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.21-13_all.deb ... Unpacking autopoint (0.21-13) ... Selecting previously unselected package binutils-arm-linux-gnueabihf. Preparing to unpack .../017-binutils-arm-linux-gnueabihf_2.41-6_amd64.deb ... Unpacking binutils-arm-linux-gnueabihf (2.41-6) ... Selecting previously unselected package gcc-13-arm-linux-gnueabihf-base:amd64. Preparing to unpack .../018-gcc-13-arm-linux-gnueabihf-base_13.2.0-6cross1_amd64.deb ... Unpacking gcc-13-arm-linux-gnueabihf-base:amd64 (13.2.0-6cross1) ... Selecting previously unselected package cpp-13-arm-linux-gnueabihf. Preparing to unpack .../019-cpp-13-arm-linux-gnueabihf_13.2.0-6cross1_amd64.deb ... Unpacking cpp-13-arm-linux-gnueabihf (13.2.0-6cross1) ... Selecting previously unselected package cpp-arm-linux-gnueabihf. Preparing to unpack .../020-cpp-arm-linux-gnueabihf_4%3a13.2.0-1_amd64.deb ... Unpacking cpp-arm-linux-gnueabihf (4:13.2.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../021-cross-config_2.6.20_all.deb ... Unpacking cross-config (2.6.20) ... Selecting previously unselected package gcc-13-cross-base. Preparing to unpack .../022-gcc-13-cross-base_13.2.0-6cross1_all.deb ... Unpacking gcc-13-cross-base (13.2.0-6cross1) ... Selecting previously unselected package libc6-armhf-cross. Preparing to unpack .../023-libc6-armhf-cross_2.37-12cross1_all.deb ... Unpacking libc6-armhf-cross (2.37-12cross1) ... Selecting previously unselected package libgcc-s1-armhf-cross. Preparing to unpack .../024-libgcc-s1-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libgcc-s1-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package libgomp1-armhf-cross. Preparing to unpack .../025-libgomp1-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libgomp1-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package libatomic1-armhf-cross. Preparing to unpack .../026-libatomic1-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libatomic1-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package libasan8-armhf-cross. Preparing to unpack .../027-libasan8-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libasan8-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package libstdc++6-armhf-cross. Preparing to unpack .../028-libstdc++6-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libstdc++6-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package libubsan1-armhf-cross. Preparing to unpack .../029-libubsan1-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libubsan1-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package libgcc-13-dev-armhf-cross. Preparing to unpack .../030-libgcc-13-dev-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libgcc-13-dev-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package gcc-13-arm-linux-gnueabihf. Preparing to unpack .../031-gcc-13-arm-linux-gnueabihf_13.2.0-6cross1_amd64.deb ... Unpacking gcc-13-arm-linux-gnueabihf (13.2.0-6cross1) ... Selecting previously unselected package gcc-arm-linux-gnueabihf. Preparing to unpack .../032-gcc-arm-linux-gnueabihf_4%3a13.2.0-1_amd64.deb ... Unpacking gcc-arm-linux-gnueabihf (4:13.2.0-1) ... Selecting previously unselected package linux-libc-dev-armhf-cross. Preparing to unpack .../033-linux-libc-dev-armhf-cross_6.5.8-1cross1_all.deb ... Unpacking linux-libc-dev-armhf-cross (6.5.8-1cross1) ... Selecting previously unselected package libc6-dev-armhf-cross. Preparing to unpack .../034-libc6-dev-armhf-cross_2.37-12cross1_all.deb ... Unpacking libc6-dev-armhf-cross (2.37-12cross1) ... Selecting previously unselected package libstdc++-13-dev-armhf-cross. Preparing to unpack .../035-libstdc++-13-dev-armhf-cross_13.2.0-6cross1_all.deb ... Unpacking libstdc++-13-dev-armhf-cross (13.2.0-6cross1) ... Selecting previously unselected package g++-13-arm-linux-gnueabihf. Preparing to unpack .../036-g++-13-arm-linux-gnueabihf_13.2.0-6cross1_amd64.deb ... Unpacking g++-13-arm-linux-gnueabihf (13.2.0-6cross1) ... Selecting previously unselected package g++-arm-linux-gnueabihf. Preparing to unpack .../037-g++-arm-linux-gnueabihf_4%3a13.2.0-1_amd64.deb ... Unpacking g++-arm-linux-gnueabihf (4:13.2.0-1) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../038-libconfig-inifiles-perl_3.000003-2_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-2) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../039-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../040-libicu72_72.1-4_amd64.deb ... Unpacking libicu72:amd64 (72.1-4) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../041-libxml2_2.9.14+dfsg-1.3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../042-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../043-libxml-sax-base-perl_1.09-3_all.deb ... Unpacking libxml-sax-base-perl (1.09-3) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../044-libxml-sax-perl_1.02+dfsg-3_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-3) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../045-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1_amd64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../046-libxml-simple-perl_2.25-2_all.deb ... Unpacking libxml-simple-perl (2.25-2) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../047-libyaml-perl_1.30-2_all.deb ... Unpacking libyaml-perl (1.30-2) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../048-libconfig-auto-perl_0.44-2_all.deb ... Unpacking libconfig-auto-perl (0.44-2) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../049-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../050-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../051-libdebian-dpkgcross-perl_2.6.20_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.20) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../052-dpkg-cross_2.6.20_all.deb ... Unpacking dpkg-cross (2.6.20) ... Selecting previously unselected package crossbuild-essential-armhf. Preparing to unpack .../053-crossbuild-essential-armhf_12.10_all.deb ... Unpacking crossbuild-essential-armhf (12.10) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../054-libdebhelper-perl_13.11.7_all.deb ... Unpacking libdebhelper-perl (13.11.7) ... Selecting previously unselected package libtool. Preparing to unpack .../055-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../056-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../057-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../058-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../060-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../061-libelf1_0.189-4_amd64.deb ... Unpacking libelf1:amd64 (0.189-4) ... Selecting previously unselected package dwz. Preparing to unpack .../062-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../063-gettext_0.21-13+b1_amd64.deb ... Unpacking gettext (0.21-13+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../064-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../065-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../066-debhelper_13.11.7_all.deb ... Unpacking debhelper (13.11.7) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../067-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../068-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../069-fontconfig-config_2.14.2-6_amd64.deb ... Unpacking fontconfig-config (2.14.2-6) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../070-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package gcc-11-base:armhf. Preparing to unpack .../071-gcc-11-base_11.4.0-5_armhf.deb ... Unpacking gcc-11-base:armhf (11.4.0-5) ... Selecting previously unselected package gcc-13-base:armhf. Preparing to unpack .../072-gcc-13-base_13.2.0-6_armhf.deb ... Unpacking gcc-13-base:armhf (13.2.0-6) ... Selecting previously unselected package libgcc-s1:armhf. Preparing to unpack .../073-libgcc-s1_13.2.0-6_armhf.deb ... Unpacking libgcc-s1:armhf (13.2.0-6) ... Selecting previously unselected package libc6:armhf. Preparing to unpack .../074-libc6_2.37-12_armhf.deb ... Unpacking libc6:armhf (2.37-12) ... Selecting previously unselected package libasan6:armhf. Preparing to unpack .../075-libasan6_11.4.0-5_armhf.deb ... Unpacking libasan6:armhf (11.4.0-5) ... Selecting previously unselected package libatomic1:armhf. Preparing to unpack .../076-libatomic1_13.2.0-6_armhf.deb ... Unpacking libatomic1:armhf (13.2.0-6) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../077-libbrotli1_1.1.0-1_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../078-libbsd0_0.11.7-4_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-4) ... Selecting previously unselected package linux-libc-dev:armhf. Preparing to unpack .../079-linux-libc-dev_6.5.10-1_armhf.deb ... Unpacking linux-libc-dev:armhf (6.5.10-1) ... Selecting previously unselected package libcrypt1:armhf. Preparing to unpack .../080-libcrypt1_1%3a4.4.36-2_armhf.deb ... Unpacking libcrypt1:armhf (1:4.4.36-2) ... Selecting previously unselected package libcrypt-dev:armhf. Preparing to unpack .../081-libcrypt-dev_1%3a4.4.36-2_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.36-2) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../082-libkrb5support0_1.20.1-5_armhf.deb ... Unpacking libkrb5support0:armhf (1.20.1-5) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../083-libcom-err2_1.47.0-2+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.0-2+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../084-libk5crypto3_1.20.1-5_armhf.deb ... Unpacking libk5crypto3:armhf (1.20.1-5) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../085-libkeyutils1_1.6.3-2_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-2) ... Selecting previously unselected package libssl3:armhf. Preparing to unpack .../086-libssl3_3.0.12-2_armhf.deb ... Unpacking libssl3:armhf (3.0.12-2) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../087-libkrb5-3_1.20.1-5_armhf.deb ... Unpacking libkrb5-3:armhf (1.20.1-5) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../088-libgssapi-krb5-2_1.20.1-5_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.20.1-5) ... Selecting previously unselected package libtirpc3:armhf. Preparing to unpack .../089-libtirpc3_1.3.3+ds-1_armhf.deb ... Unpacking libtirpc3:armhf (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../090-libnsl2_1.3.0-3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3) ... Selecting previously unselected package libtirpc-dev:armhf. Preparing to unpack .../091-libtirpc-dev_1.3.3+ds-1_armhf.deb ... Unpacking libtirpc-dev:armhf (1.3.3+ds-1) ... Selecting previously unselected package libnsl-dev:armhf. Preparing to unpack .../092-libnsl-dev_1.3.0-3_armhf.deb ... Unpacking libnsl-dev:armhf (1.3.0-3) ... Selecting previously unselected package libc6-dev:armhf. Preparing to unpack .../093-libc6-dev_2.37-12_armhf.deb ... Unpacking libc6-dev:armhf (2.37-12) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../094-libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../095-libpng16-16_1.6.40-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.40-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../096-libfreetype6_2.13.2+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../097-libfontconfig1_2.14.2-6_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.2-6) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../098-libpixman-1-0_0.42.2-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../099-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../100-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../101-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../102-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../103-libx11-6_2%3a1.8.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../104-libxcb-render0_1.15-1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../105-libxcb-shm0_1.15-1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.15-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../106-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../107-libxrender1_1%3a0.9.10-1.1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../108-libcairo2_1.18.0-1_amd64.deb ... Unpacking libcairo2:amd64 (1.18.0-1) ... Selecting previously unselected package libgomp1:armhf. Preparing to unpack .../109-libgomp1_13.2.0-6_armhf.deb ... Unpacking libgomp1:armhf (13.2.0-6) ... Selecting previously unselected package libstdc++6:armhf. Preparing to unpack .../110-libstdc++6_13.2.0-6_armhf.deb ... Unpacking libstdc++6:armhf (13.2.0-6) ... Selecting previously unselected package libubsan1:armhf. Preparing to unpack .../111-libubsan1_13.2.0-6_armhf.deb ... Unpacking libubsan1:armhf (13.2.0-6) ... Selecting previously unselected package libgcc-11-dev:armhf. Preparing to unpack .../112-libgcc-11-dev_11.4.0-5_armhf.deb ... Unpacking libgcc-11-dev:armhf (11.4.0-5) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../113-libglib2.0-0_2.78.1-3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.78.1-3) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../114-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../115-libharfbuzz0b_8.0.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (8.0.1-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../116-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../117-libice6_2%3a1.0.10-1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1) ... Selecting previously unselected package libkpathsea6:amd64. Preparing to unpack .../118-libkpathsea6_2023.20230311.66589-7_amd64.deb ... Unpacking libkpathsea6:amd64 (2023.20230311.66589-7) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../119-libpaper1_1.1.29_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../120-libpaper-utils_1.1.29_amd64.deb ... Unpacking libpaper-utils (1.1.29) ... Selecting previously unselected package libpotrace0:amd64. Preparing to unpack .../121-libpotrace0_1.16-2_amd64.deb ... Unpacking libpotrace0:amd64 (1.16-2) ... Selecting previously unselected package libptexenc1:amd64. Preparing to unpack .../122-libptexenc1_2023.20230311.66589-7_amd64.deb ... Unpacking libptexenc1:amd64 (2023.20230311.66589-7) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../123-libsm6_2%3a1.2.3-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1) ... Selecting previously unselected package libstdc++-11-dev:armhf. Preparing to unpack .../124-libstdc++-11-dev_11.4.0-5_armhf.deb ... Unpacking libstdc++-11-dev:armhf (11.4.0-5) ... Selecting previously unselected package libsynctex2:amd64. Preparing to unpack .../125-libsynctex2_2023.20230311.66589-7_amd64.deb ... Unpacking libsynctex2:amd64 (2023.20230311.66589-7) ... Selecting previously unselected package libteckit0:amd64. Preparing to unpack .../126-libteckit0_2.5.11+ds1-1+b1_amd64.deb ... Unpacking libteckit0:amd64 (2.5.11+ds1-1+b1) ... Selecting previously unselected package libtexlua53-5:amd64. Preparing to unpack .../127-libtexlua53-5_2023.20230311.66589-7_amd64.deb ... Unpacking libtexlua53-5:amd64 (2023.20230311.66589-7) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../128-libxt6_1%3a1.2.1-1.1_amd64.deb ... Unpacking libxt6:amd64 (1:1.2.1-1.1) ... Selecting previously unselected package libxmu6:amd64. Preparing to unpack .../129-libxmu6_2%3a1.1.3-3_amd64.deb ... Unpacking libxmu6:amd64 (2:1.1.3-3) ... Selecting previously unselected package libxpm4:amd64. Preparing to unpack .../130-libxpm4_1%3a3.5.17-1_amd64.deb ... Unpacking libxpm4:amd64 (1:3.5.17-1) ... Selecting previously unselected package libxaw7:amd64. Preparing to unpack .../131-libxaw7_2%3a1.0.14-1_amd64.deb ... Unpacking libxaw7:amd64 (2:1.0.14-1) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../132-libxi6_2%3a1.8-1+b1_amd64.deb ... Unpacking libxi6:amd64 (2:1.8-1+b1) ... Selecting previously unselected package libzzip-0-13:amd64. Preparing to unpack .../133-libzzip-0-13_0.13.72+dfsg.1-1.1_amd64.deb ... Unpacking libzzip-0-13:amd64 (0.13.72+dfsg.1-1.1) ... Selecting previously unselected package t1utils. Preparing to unpack .../134-t1utils_1.41-4_amd64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package tex-common. Preparing to unpack .../135-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../136-texlive-binaries_2023.20230311.66589-7_amd64.deb ... Unpacking texlive-binaries (2023.20230311.66589-7) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../137-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package texlive-base. Preparing to unpack .../138-texlive-base_2023.20231007-1_all.deb ... Unpacking texlive-base (2023.20231007-1) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../139-texlive-latex-base_2023.20231007-1_all.deb ... Unpacking texlive-latex-base (2023.20231007-1) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../140-texlive-latex-recommended_2023.20231007-1_all.deb ... Unpacking texlive-latex-recommended (2023.20231007-1) ... Selecting previously unselected package zlib1g:armhf. Preparing to unpack .../141-zlib1g_1%3a1.2.13.dfsg-3_armhf.deb ... Unpacking zlib1g:armhf (1:1.2.13.dfsg-3) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../142-zlib1g-dev_1%3a1.2.13.dfsg-3_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-3) ... Selecting previously unselected package sbuild-build-depends-main-dummy:armhf. Preparing to unpack .../143-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-2) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up gcc-11-base:armhf (11.4.0-5) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libc6-armhf-cross (2.37-12cross1) ... Setting up libicu72:amd64 (72.1-4) ... Setting up bsdextrautils (2.39.2-5) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.78.1-3) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.7) ... Setting up libbrotli1:amd64 (1.1.0-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of restart. Setting up libmagic1:amd64 (1:5.45-2) ... Setting up linux-libc-dev:armhf (6.5.10-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-13+b1) ... Setting up m4 (1.4.19-4) ... Setting up libzzip-0-13:amd64 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.45-2) ... Setting up libyaml-perl (1.30-2) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up gcc-13-base:armhf (13.2.0-6) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:amd64 (2.5.11+ds1-1+b1) ... Setting up gcc-13-cross-base (13.2.0-6cross1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2023.20230311.66589-7) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.40-2) ... Setting up linux-libc-dev-armhf-cross (6.5.8-1cross1) ... Setting up autopoint (0.21-13) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:amd64 (2023.20230311.66589-7) ... Setting up autoconf (2.71-3) ... Setting up gcc-13-arm-linux-gnueabihf-base:amd64 (13.2.0-6cross1) ... Setting up sensible-utils (0.0.20) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up binutils-arm-linux-gnueabihf (2.41-6) ... Setting up libelf1:amd64 (0.189-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3) ... 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 liblocale-gettext-perl (1.07-6) ... Setting up libsynctex2:amd64 (2023.20230311.66589-7) ... Setting up libpotrace0:amd64 (1.16-2) ... 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 libgomp1-armhf-cross (13.2.0-6cross1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-13+b1) ... Setting up cpp-13-arm-linux-gnueabihf (13.2.0-6cross1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libgcc-s1-armhf-cross (13.2.0-6cross1) ... Setting up fontconfig-config (2.14.2-6) ... Setting up libc6-dev-armhf-cross (2.37-12cross1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libatomic1-armhf-cross (13.2.0-6cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libstdc++6-armhf-cross (13.2.0-6cross1) ... Setting up libptexenc1:amd64 (2023.20230311.66589-7) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1) ... Setting up libubsan1-armhf-cross (13.2.0-6cross1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libharfbuzz0b:amd64 (8.0.1-1) ... Setting up libfontconfig1:amd64 (2.14.2-6) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up cpp-arm-linux-gnueabihf (4:13.2.0-1) ... Setting up libasan8-armhf-cross (13.2.0-6cross1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up libxpm4:amd64 (1:3.5.17-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. 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 libcairo2:amd64 (1.18.0-1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libgcc-13-dev-armhf-cross (13.2.0-6cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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 libxmu6:amd64 (2:1.1.3-3) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libstdc++-13-dev-armhf-cross (13.2.0-6cross1) ... Setting up debhelper (13.11.7) ... Setting up libxaw7:amd64 (2:1.0.14-1) ... Setting up gcc-13-arm-linux-gnueabihf (13.2.0-6cross1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up texlive-binaries (2023.20230311.66589-7) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2023.20231007-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up gcc-arm-linux-gnueabihf (4:13.2.0-1) ... Setting up g++-13-arm-linux-gnueabihf (13.2.0-6cross1) ... Setting up g++-arm-linux-gnueabihf (4:13.2.0-1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up texlive-latex-base (2023.20231007-1) ... Setting up texlive-latex-recommended (2023.20231007-1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-armhf (12.10) ... Setting up libgcc-s1:armhf (13.2.0-6) ... Setting up libc6:armhf (2.37-12) ... Setting up libstdc++6:armhf (13.2.0-6) ... Setting up libkeyutils1:armhf (1.6.3-2) ... Setting up libssl3:armhf (3.0.12-2) ... Setting up zlib1g:armhf (1:1.2.13.dfsg-3) ... Setting up libcrypt1:armhf (1:4.4.36-2) ... Setting up libcom-err2:armhf (1.47.0-2+b1) ... Setting up libgomp1:armhf (13.2.0-6) ... Setting up libasan6:armhf (11.4.0-5) ... Setting up libkrb5support0:armhf (1.20.1-5) ... Setting up libatomic1:armhf (13.2.0-6) ... Setting up libk5crypto3:armhf (1.20.1-5) ... Setting up libubsan1:armhf (13.2.0-6) ... Setting up libgcc-11-dev:armhf (11.4.0-5) ... Setting up libcrypt-dev:armhf (1:4.4.36-2) ... Setting up libkrb5-3:armhf (1.20.1-5) ... Setting up libgssapi-krb5-2:armhf (1.20.1-5) ... Setting up libtirpc3:armhf (1.3.3+ds-1) ... Setting up libtirpc-dev:armhf (1.3.3+ds-1) ... Setting up libnsl2:armhf (1.3.0-3) ... Setting up libnsl-dev:armhf (1.3.0-3) ... Setting up libc6-dev:armhf (2.37-12) ... Setting up libstdc++-11-dev:armhf (11.4.0-5) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.37-12) ... 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 (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64) Toolchain package versions: binutils_2.41-6 dpkg-dev_1.22.1 g++-11_11.4.0-5 g++-13_13.2.0-6 gcc-11_11.4.0-5 gcc-13_13.2.0-6 libc6-dev_2.37-12 libstdc++-11-dev_11.4.0-5 libstdc++-13-dev_13.2.0-6 libstdc++-13-dev-armhf-cross_13.2.0-6cross1 libstdc++6_13.2.0-6 libstdc++6-armhf-cross_13.2.0-6cross1 linux-libc-dev_6.5.10-1 Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.2 bash_5.2.15-2+b6 binutils_2.41-6 binutils-arm-linux-gnueabihf_2.41-6 binutils-common_2.41-6 binutils-x86-64-linux-gnu_2.41-6 bsdextrautils_2.39.2-5 bsdutils_1:2.39.2-5 build-essential_12.10 bzip2_1.0.8-5+b1 coreutils_9.4-2+b1 cpp_4:13.2.0-1 cpp-11_11.4.0-5 cpp-13_13.2.0-6 cpp-13-arm-linux-gnueabihf_13.2.0-6cross1 cpp-arm-linux-gnueabihf_4:13.2.0-1 cross-config_2.6.20 crossbuild-essential-armhf_12.10 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.7 debian-archive-keyring_2023.4 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.1 dpkg-cross_2.6.20 dpkg-dev_1.22.1 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 g++_4:13.2.0-1 g++-11_11.4.0-5 g++-13_13.2.0-6 g++-13-arm-linux-gnueabihf_13.2.0-6cross1 g++-arm-linux-gnueabihf_4:13.2.0-1 gcc_4:13.2.0-1 gcc-11_11.4.0-5 gcc-11-base_11.4.0-5 gcc-12-base_12.3.0-11 gcc-13_13.2.0-6 gcc-13-arm-linux-gnueabihf_13.2.0-6cross1 gcc-13-arm-linux-gnueabihf-base_13.2.0-6cross1 gcc-13-base_13.2.0-6 gcc-13-cross-base_13.2.0-6cross1 gcc-9-base_9.5.0-4 gcc-arm-linux-gnueabihf_4:13.2.0-1 gettext_0.21-13+b1 gettext-base_0.21-13+b1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan6_11.4.0-5 libasan8_13.2.0-6 libasan8-armhf-cross_13.2.0-6cross1 libatomic1_13.2.0-6 libatomic1-armhf-cross_13.2.0-6cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6 libblkid1_2.39.2-5 libbrotli1_1.1.0-1 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b1 libc-bin_2.37-12 libc-dev-bin_2.37-12 libc6_2.37-12 libc6-armhf-cross_2.37-12cross1 libc6-dev_2.37-12 libc6-dev-armhf-cross_2.37-12cross1 libcairo2_1.18.0-1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-4 libcc1-0_13.2.0-6 libcom-err2_1.47.0-2+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6 libctf0_2.41-6 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.7 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.1 libelf1_0.189-4 libexpat1_2.5.0-2 libext2fs2_1.47.0-2+b1 libfakeroot_1.32.2-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libfontconfig1_2.14.2-6 libfreetype6_2.13.2+dfsg-1 libgcc-11-dev_11.4.0-5 libgcc-13-dev_13.2.0-6 libgcc-13-dev-armhf-cross_13.2.0-6cross1 libgcc-s1_13.2.0-6 libgcc-s1-armhf-cross_13.2.0-6cross1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libglib2.0-0_2.78.1-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4+b1 libgomp1_13.2.0-6 libgomp1-armhf-cross_13.2.0-6cross1 libgpg-error0_1.47-2 libgprofng0_2.41-6 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20.1-5 libharfbuzz0b_8.0.1-1 libhogweed6_3.9.1-2 libhwasan0_13.2.0-6 libice6_2:1.0.10-1 libicu72_72.1-4 libidn2-0_2.3.4-1+b1 libio-string-perl_1.08-4 libisl23_0.26-3 libitm1_13.2.0-6 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkpathsea6_2023.20230311.66589-7 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 liblocale-gettext-perl_1.07-6 liblsan0_13.2.0-6 liblz4-1_1.9.4-1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-5 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libnettle8_3.9.1-2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpaper-utils_1.1.29 libpaper1_1.1.29 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.40-2 libpotrace0_1.16-2 libptexenc1_2023.20230311.66589-7 libquadmath0_13.2.0-6 libseccomp2_2.5.4-2 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6 libsm6_2:1.2.3-1 libsmartcols1_2.39.2-5 libss2_1.47.0-2+b1 libssl3_3.0.12-2 libstdc++-11-dev_11.4.0-5 libstdc++-13-dev_13.2.0-6 libstdc++-13-dev-armhf-cross_13.2.0-6cross1 libstdc++6_13.2.0-6 libstdc++6-armhf-cross_13.2.0-6cross1 libsub-override-perl_0.09-4 libsynctex2_2023.20230311.66589-7 libsystemd0_254.5-1 libtasn1-6_4.19.0-3 libteckit0_2.5.11+ds1-1+b1 libtexlua53-5_2023.20230311.66589-7 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libtsan0_11.4.0-5 libtsan2_13.2.0-6 libubsan1_13.2.0-6 libubsan1-armhf-cross_13.2.0-6cross1 libuchardet0_0.0.7-1 libudev1_254.5-1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-5 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1+b1 libxi6_2:1.8-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3 libxmu6_2:1.1.3-3 libxpm4_1:3.5.17-1 libxrender1_1:0.9.10-1.1 libxt6_1:1.2.1-1.1 libxxhash0_0.8.2-2 libyaml-perl_1.30-2 libzstd1_1.5.5+dfsg2-2 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_6.5.10-1 linux-libc-dev-armhf-cross_6.5.8-1cross1 login_1:4.13+dfsg1-3 logsave_1.47.0-2+b1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 mount_2.39.2-5 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-9 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-3 t1utils_1.41-4 tar_1.34+dfsg-1.2 tex-common_6.18 texlive-base_2023.20231007-1 texlive-binaries_2023.20230311.66589-7 texlive-latex-base_2023.20231007-1 texlive-latex-recommended_2023.20231007-1 tzdata_2023c-10 ucf_3.0043+nmu1 usrmerge_38 util-linux_2.39.2-5 util-linux-extra_2.39.2-5 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3 +------------------------------------------------------------------------------+ | 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+dfsg1-8 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/dzerbino/velvet Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/velvet Vcs-Git: https://salsa.debian.org/med-team/velvet.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, texlive-latex-base, texlive-latex-recommended Package-List: velvet deb science optional arch=any velvet-example deb science optional arch=all velvet-long deb science optional arch=any velvet-tests deb science optional arch=all Checksums-Sha1: f5ade530e902bdf69532648429a91c00f3a1ad2d 13630488 velvet_1.2.10+dfsg1.orig.tar.xz d038bf3d2c9473b711b6582867fb3c0e7d43b360 17152 velvet_1.2.10+dfsg1-8.debian.tar.xz Checksums-Sha256: 368d760ad56ffa010a2ae72b25d46680ecb7ad8cc573cf6c389848c87b32ee26 13630488 velvet_1.2.10+dfsg1.orig.tar.xz dac824d414948cd356c22459f0f66180e6be86209346da4e67b72227d68bd871 17152 velvet_1.2.10+dfsg1-8.debian.tar.xz Files: 7a58a6d75cdc8b89d1c605033050bbcf 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 867f3efcbd489623ce46364ef2a3ad2f 17152 velvet_1.2.10+dfsg1-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOGXSMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHK9g/9HYJ/3hQ5uVdIpwOZuU1i2Pktq9Aptny4 4HJuNPJ7hf1+oS4/oJ6pT60AXHwBaQIYhf4AtQdD7tuLHXe76KXPCso50k9Umrou T5c9SRgOkzKjq70qYrIxZYorzRf2UH5nBj5fYeg4czcXplkqknUsnf0Ukqn6vp/g zjPKsCDnWvRbfmThvayZjTgykVuNlxvjRWqUUI0CCNNUnsZIo9+STjeCIqLc81Uy CfCEcdu6aROhqqpLCtvbF32We2wETYVFnS73WRmvNtJQ7iInKr/9y9TavSoixZ5J zoZT9vD4lloOZ4daYVrjKlkf+MgdmZYyFE8pSgrnikVwbsShbL3SC8YBe4E1BDEH uFwnCaWEbRquRBdVnWHZFsK78uQq6t8W5zpRBz2ItwEPWgzB5JncJMYVJE/rO2h3 U4L7/ajQTzqckJ6kpCHVpDVBsQMssyOKgFKXNhbF05Ozcf6zTtadmFpK1nJM2ZL1 4pqjPkz1OL2SmhrIW9+1LCowAdGWO0WDKW4AxenR1YurqcEHt/iw6TnOttX5ya2g Fsr8brI+cJRjZO5fLO5oFtdsSl1W/xWY8JV0dBTilfm+fNHyWQ0Ej4pBu1HLXTFh jOVkS6OdpnNq0aDgEoPefkJ6eZuPeko53a8DHg7KlzNEHkAQ7AFDkkE+HPOPIwD8 XR+1Mbs64zY= =Vpgu -----END PGP SIGNATURE----- gpgv: Signature made Tue Nov 29 19:27:31 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-8.dsc: no acceptable signature found dpkg-source: info: extracting velvet in /<> dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf 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.Pcd7yfXPzC/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-63d8ee55-69bc-4adc-a643-6814e78a9723 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf 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 armhf debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory rm: cannot remove './velvet*': No such file or directory make[2]: [Makefile:45: clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory '/<>' rm -rf zlib rm -rf third-party rm -rf debian.upstream rm -f *.pdf find -name '._*' -delete rm -rf contrib/MetaVelvet* rm -rf contrib/VelvetOptimiser* make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' touch zlib #Make _long version dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2023-06-01> patch level 1 L3 programming layer <2023-08-29> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.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/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/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Manual.aux. (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) No file Manual.toc. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 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 (1.49698pt 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 (1.49698pt 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 (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt 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 (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 331. Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 354. LaTeX Warning: Reference `sec:kmercov' on page 8 undefined on input line 358. LaTeX Warning: Reference `sec:expcov' on page 8 undefined on input line 358. Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [8] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] LaTeX Warning: Reference `sec:hashing' on page 9 undefined on input line 377. LaTeX Warning: Reference `sec:kmercov' on page 9 undefined on input line 379. LaTeX Warning: Reference `sec:pairedformat' on page 9 undefined on input line 3 95. Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [9] [10] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:amos' on page 11 undefined on input line 455. Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 11 undefined on input line 470. Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set LaTeX Warning: Reference `sec:paper' on page 11 undefined on input line 499. [11] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [12] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [13] LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 593. LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 605. Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 615. [14] Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 642. Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 683 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 695. LaTeX Warning: Reference `sec:kmercov' on page 16 undefined on input line 695. [16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /<>/debian/.debhelper/generated/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) >/velv et-1.2.10+dfsg1/debian/.debhelper/generated/_source/home/.texlive2023/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk> Output written on Manual.pdf (21 pages, 432052 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2023-06-01> patch level 1 L3 programming layer <2023-08-29> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.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/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/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./Manual.out ) (./Manual.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 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 (1.49698pt 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 (1.49698pt 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 (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt 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 (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt 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/.texlive2023/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk> Output written on Manual.pdf (22 pages, 439986 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2023-06-01> patch level 1 L3 programming layer <2023-08-29> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (23.7252pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_seque nces.fa[] [5] (./Columbus_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /<>/debian/.debhelper/generated/_source/home/.texlive2023/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/.texlive2023/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk> Output written on Columbus_manual.pdf (5 pages, 88580 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/<>' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -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-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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: | ^~~~ src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 arm-linux-gnueabihf-gcc -g -O2 -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-gnueabihf-gcc -g -O2 -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 dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-8_armhf.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-8_armhf.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb'. dpkg-genbuildinfo --build=any -O../velvet_1.2.10+dfsg1-8_armhf.buildinfo dpkg-genchanges --build=any -O../velvet_1.2.10+dfsg1-8_armhf.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 2023-11-10T23:07:27Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ velvet_1.2.10+dfsg1-8_armhf.changes: ------------------------------------ Format: 1.8 Date: Tue, 29 Nov 2022 20:22:14 +0100 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 1.2.10+dfsg1-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: velvet - Nucleic acid sequence assembler for very short reads velvet-long - Nucleic acid sequence assembler for very short reads, long versio Changes: velvet (1.2.10+dfsg1-8) unstable; urgency=medium . * Apply multi-arch hints. + velvet-tests: Add Multi-Arch: foreign. * Point Homepage to Github since original homepage vanished * Fix watch file * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * Fix typo in debian/rules rules: override_dh_auto_clean ⇒ override_dh_auto_clean, override_dh_auto_build ⇒ override_dh_auto_build, override_dh_install ⇒ override_dh_install, override_dh_install ⇒ override_mh_install, override_dh_compress ⇒ override_dh_compress Checksums-Sha1: 233203e03b144931f5216e8b2093f8b76db33134 895016 velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb f0ccff7db3bc639ce589e0a0a892706299a41edb 2013152 velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb a9e8fc1f53ca0e584087dffac5926a76b40a9502 199960 velvet-long_1.2.10+dfsg1-8_armhf.deb 2a6eafad88d8a80ea70841f9fe8c23a91ab0875c 7366 velvet_1.2.10+dfsg1-8_armhf.buildinfo b664f2ff9a6c4aacbb5bdb6aef7ac883c0079a0c 640852 velvet_1.2.10+dfsg1-8_armhf.deb Checksums-Sha256: fdbdbf26a18582b8825a2a85ca0454169eed335aa0d0a142be330f920b8298de 895016 velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb 18d68f61550cae19f84533b2c1c62a33af2dd146f259d6f9cb78db99837bbe36 2013152 velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb 90e0b39246d088f6670b13bd8c9d543214c3e3482e6b474eef93b8b051a58d15 199960 velvet-long_1.2.10+dfsg1-8_armhf.deb d48a1b0d9637afe4a0425afe21a1a0595535a6ef5e9b2eb9621119f0eca5fa54 7366 velvet_1.2.10+dfsg1-8_armhf.buildinfo caed1f0843ec56fd4432e0f35094fc723bc3700d11f9ff2d01da09bcd679bb28 640852 velvet_1.2.10+dfsg1-8_armhf.deb Files: 83b8d08d4b32244e7d39ec131fd3b574 895016 debug optional velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb 8dafceaf741e6f21dd3998dec73e6888 2013152 debug optional velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb 9d31dbf3bc8eaf779abdf34009deb411 199960 science optional velvet-long_1.2.10+dfsg1-8_armhf.deb abc99ae999797636d9c9ac4d410ff6f1 7366 science optional velvet_1.2.10+dfsg1-8_armhf.buildinfo eeacda2ae10109c4160c9d2dc011d001 640852 science optional velvet_1.2.10+dfsg1-8_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Architecture: armhf Version: 1.2.10+dfsg1-8 Checksums-Md5: 83b8d08d4b32244e7d39ec131fd3b574 895016 velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb 8dafceaf741e6f21dd3998dec73e6888 2013152 velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb 9d31dbf3bc8eaf779abdf34009deb411 199960 velvet-long_1.2.10+dfsg1-8_armhf.deb eeacda2ae10109c4160c9d2dc011d001 640852 velvet_1.2.10+dfsg1-8_armhf.deb Checksums-Sha1: 233203e03b144931f5216e8b2093f8b76db33134 895016 velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb f0ccff7db3bc639ce589e0a0a892706299a41edb 2013152 velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb a9e8fc1f53ca0e584087dffac5926a76b40a9502 199960 velvet-long_1.2.10+dfsg1-8_armhf.deb b664f2ff9a6c4aacbb5bdb6aef7ac883c0079a0c 640852 velvet_1.2.10+dfsg1-8_armhf.deb Checksums-Sha256: fdbdbf26a18582b8825a2a85ca0454169eed335aa0d0a142be330f920b8298de 895016 velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb 18d68f61550cae19f84533b2c1c62a33af2dd146f259d6f9cb78db99837bbe36 2013152 velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb 90e0b39246d088f6670b13bd8c9d543214c3e3482e6b474eef93b8b051a58d15 199960 velvet-long_1.2.10+dfsg1-8_armhf.deb caed1f0843ec56fd4432e0f35094fc723bc3700d11f9ff2d01da09bcd679bb28 640852 velvet_1.2.10+dfsg1-8_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 10 Nov 2023 23:07:27 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.2), bash (= 5.2.15-2+b6), binutils (= 2.41-6), binutils-common (= 2.41-6), binutils-x86-64-linux-gnu (= 2.41-6), bsdextrautils (= 2.39.2-5), bsdutils (= 1:2.39.2-5), build-essential (= 12.10), bzip2 (= 1.0.8-5+b1), coreutils (= 9.4-2+b1), cpp (= 4:13.2.0-1), cpp-11 (= 11.4.0-5), cpp-13 (= 13.2.0-6), dash (= 0.5.12-6), debconf (= 1.5.82), debhelper (= 13.11.7), debianutils (= 5.14), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.1), dpkg-dev (= 1.22.1), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), fontconfig-config (= 2.14.2-6), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), g++ (= 4:13.2.0-1), g++-13 (= 13.2.0-6), gcc (= 4:13.2.0-1), gcc-11 (= 11.4.0-5), gcc-11-base (= 11.4.0-5), gcc-13 (= 13.2.0-6), gcc-13-base (= 13.2.0-6), gettext (= 0.21-13+b1), gettext-base (= 0.21-13+b1), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1), hostname (= 3.23+nmu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.4.0-5), libasan8 (= 13.2.0-6), libatomic1 (= 13.2.0-6), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-6), libblkid1 (= 2.39.2-5), libbrotli1 (= 1.1.0-1), libbsd0 (= 0.11.7-4), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.37-12), libc-dev-bin (= 2.37-12), libc6 (= 2.37-12), libc6-dev (= 2.37-12), libcairo2 (= 1.18.0-1), libcap-ng0 (= 0.8.3-1+b3), libcap2 (= 1:2.66-4), libcc1-0 (= 13.2.0-6), libcom-err2 (= 1.47.0-2+b1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-6), libctf0 (= 2.41-6), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271), libdebhelper-perl (= 13.11.7), libdpkg-perl (= 1.22.1), libelf1 (= 0.189-4), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.14.2-6), libfreetype6 (= 2.13.2+dfsg-1), libgcc-11-dev (= 11.4.0-5), libgcc-13-dev (= 13.2.0-6), libgcc-s1 (= 13.2.0-6), libgcrypt20 (= 1.10.2-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libglib2.0-0 (= 2.78.1-3), libgmp10 (= 2:6.3.0+dfsg-2), libgomp1 (= 13.2.0-6), libgpg-error0 (= 1.47-2), libgprofng0 (= 2.41-6), libgraphite2-3 (= 1.3.14-1), libgssapi-krb5-2 (= 1.20.1-5), libharfbuzz0b (= 8.0.1-1), libhwasan0 (= 13.2.0-6), libice6 (= 2:1.0.10-1), libicu72 (= 72.1-4), libisl23 (= 0.26-3), libitm1 (= 13.2.0-6), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2), libkpathsea6 (= 2023.20230311.66589-7), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblsan0 (= 13.2.0-6), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.4-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmount1 (= 2.39.2-5), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-9.1), libpam-modules-bin (= 1.5.2-9.1), libpam-runtime (= 1.5.2-9.1), libpam0g (= 1.5.2-9.1), libpaper-utils (= 1.1.29), libpaper1 (= 1.1.29), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-9), libpipeline1 (= 1.5.7-1), libpixman-1-0 (= 0.42.2-1), libpng16-16 (= 1.6.40-2), libpotrace0 (= 1.16-2), libptexenc1 (= 2023.20230311.66589-7), libquadmath0 (= 13.2.0-6), libseccomp2 (= 2.5.4-2), libselinux1 (= 3.5-1), libsframe1 (= 2.41-6), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.39.2-5), libssl3 (= 3.0.12-2), libstdc++-13-dev (= 13.2.0-6), libstdc++6 (= 13.2.0-6), libsub-override-perl (= 0.09-4), libsynctex2 (= 2023.20230311.66589-7), libsystemd0 (= 254.5-1), libteckit0 (= 2.5.11+ds1-1+b1), libtexlua53-5 (= 2023.20230311.66589-7), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4+20231016-1), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-7), libtsan0 (= 11.4.0-5), libtsan2 (= 13.2.0-6), libubsan1 (= 13.2.0-6), libuchardet0 (= 0.0.7-1), libudev1 (= 254.5-1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-5), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1), libxaw7 (= 2:1.0.14-1), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.4-1+b1), libxi6 (= 2:1.8-1+b1), libxml2 (= 2.9.14+dfsg-1.3), libxmu6 (= 2:1.1.3-3), libxpm4 (= 1:3.5.17-1), libxrender1 (= 1:0.9.10-1.1), libxt6 (= 1:1.2.1-1.1), libzstd1 (= 1.5.5+dfsg2-2), libzzip-0-13 (= 0.13.72+dfsg.1-1.1), linux-libc-dev (= 6.5.10-1), login (= 1:4.13+dfsg1-3), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.0-1), mawk (= 1.3.4.20230808-1), ncurses-base (= 6.4+20231016-1), ncurses-bin (= 6.4+20231016-1), patch (= 2.7.6-7), perl (= 5.36.0-9), perl-base (= 5.36.0-9), perl-modules-5.36 (= 5.36.0-9), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3), t1utils (= 1.41-4), tar (= 1.34+dfsg-1.2), tex-common (= 6.18), texlive-base (= 2023.20231007-1), texlive-binaries (= 2023.20230311.66589-7), texlive-latex-base (= 2023.20231007-1), texlive-latex-recommended (= 2023.20231007-1), ucf (= 3.0043+nmu1), usrmerge (= 38), util-linux (= 2.39.2-5), x11-common (= 1:7.7+23), xdg-utils (= 1.1.3-4.1), xz-utils (= 5.4.4-0.1), zlib1g (= 1:1.2.13.dfsg-3), zlib1g-dev (= 1:1.2.13.dfsg-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1669749734" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ velvet-dbgsym_1.2.10+dfsg1-8_armhf.deb -------------------------------------- new Debian package, version 2.0. size 895016 bytes: control archive=748 bytes. 503 bytes, 12 lines control 510 bytes, 5 lines md5sums Package: velvet-dbgsym Source: velvet Version: 1.2.10+dfsg1-8 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 996 Depends: velvet (= 1.2.10+dfsg1-8) Section: debug Priority: optional Description: debug symbols for velvet Build-Ids: 1af660fe0c1145836b58d574cacf41b1661122f6 2f85e80adc9156b5e0623f61873a23f56e1da580 39de3211eeb55c8c523483607fe21e49408c5224 6ccdb08698b05dae6c27e80d83e807a1c5902972 drwxr-xr-x root/root 0 2022-11-29 19:22 ./ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/1a/ -rw-r--r-- root/root 100068 2022-11-29 19:22 ./usr/lib/debug/.build-id/1a/f660fe0c1145836b58d574cacf41b1661122f6.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/2f/ -rw-r--r-- root/root 381792 2022-11-29 19:22 ./usr/lib/debug/.build-id/2f/85e80adc9156b5e0623f61873a23f56e1da580.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/39/ -rw-r--r-- root/root 97132 2022-11-29 19:22 ./usr/lib/debug/.build-id/39/de3211eeb55c8c523483607fe21e49408c5224.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/6c/ -rw-r--r-- root/root 381804 2022-11-29 19:22 ./usr/lib/debug/.build-id/6c/cdb08698b05dae6c27e80d83e807a1c5902972.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ -rw-r--r-- root/root 42440 2022-11-29 19:22 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/velvet.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-11-29 19:22 ./usr/share/doc/velvet-dbgsym -> velvet velvet-long-dbgsym_1.2.10+dfsg1-8_armhf.deb ------------------------------------------- new Debian package, version 2.0. size 2013152 bytes: control archive=1056 bytes. 765 bytes, 12 lines control 1151 bytes, 11 lines md5sums Package: velvet-long-dbgsym Source: velvet Version: 1.2.10+dfsg1-8 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2405 Depends: velvet-long (= 1.2.10+dfsg1-8) Section: debug Priority: optional Description: debug symbols for velvet-long Build-Ids: 1062da0e57d850c6eb0ec9ccf6b3940e2ab5db7e 14c2a873340fb13b27229845d8ec7bd183197cd7 1546a22b3004b5f8c97da0d7fe2fc13c04bdecd1 1978a055d0ef49c9ae50ab6398d01b34a86b2030 2c3ade3d32e77fe5c86df9643b6a5640613cafe2 39e827a839915a36cec0b050dc91c927eeb199f3 5321e5012be29b4ac734c55c260a7a4635833ae2 d662dcdcfe70ac9eb0e865e7bd8c72ebfe8601a1 dddd25741858adc45d82117f74f27a150a6c3f43 df1040602addc71e2a576141f57f3e264a1ab72a drwxr-xr-x root/root 0 2022-11-29 19:22 ./ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/10/ -rw-r--r-- root/root 96840 2022-11-29 19:22 ./usr/lib/debug/.build-id/10/62da0e57d850c6eb0ec9ccf6b3940e2ab5db7e.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/14/ -rw-r--r-- root/root 381372 2022-11-29 19:22 ./usr/lib/debug/.build-id/14/c2a873340fb13b27229845d8ec7bd183197cd7.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 381440 2022-11-29 19:22 ./usr/lib/debug/.build-id/15/46a22b3004b5f8c97da0d7fe2fc13c04bdecd1.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/19/ -rw-r--r-- root/root 96924 2022-11-29 19:22 ./usr/lib/debug/.build-id/19/78a055d0ef49c9ae50ab6398d01b34a86b2030.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/2c/ -rw-r--r-- root/root 97312 2022-11-29 19:22 ./usr/lib/debug/.build-id/2c/3ade3d32e77fe5c86df9643b6a5640613cafe2.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/39/ -rw-r--r-- root/root 381220 2022-11-29 19:22 ./usr/lib/debug/.build-id/39/e827a839915a36cec0b050dc91c927eeb199f3.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/53/ -rw-r--r-- root/root 381192 2022-11-29 19:22 ./usr/lib/debug/.build-id/53/21e5012be29b4ac734c55c260a7a4635833ae2.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/d6/ -rw-r--r-- root/root 97168 2022-11-29 19:22 ./usr/lib/debug/.build-id/d6/62dcdcfe70ac9eb0e865e7bd8c72ebfe8601a1.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/dd/ -rw-r--r-- root/root 97124 2022-11-29 19:22 ./usr/lib/debug/.build-id/dd/dd25741858adc45d82117f74f27a150a6c3f43.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.build-id/df/ -rw-r--r-- root/root 380868 2022-11-29 19:22 ./usr/lib/debug/.build-id/df/1040602addc71e2a576141f57f3e264a1ab72a.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ -rw-r--r-- root/root 44040 2022-11-29 19:22 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/velvet-long.debug drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-11-29 19:22 ./usr/share/doc/velvet-long-dbgsym -> velvet-long velvet-long_1.2.10+dfsg1-8_armhf.deb ------------------------------------ new Debian package, version 2.0. size 199960 bytes: control archive=1456 bytes. 999 bytes, 22 lines control 1499 bytes, 23 lines md5sums Package: velvet-long Source: velvet Version: 1.2.10+dfsg1-8 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1290 Depends: libc6 (>= 2.34), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2), velvet Section: science Priority: optional Homepage: https://github.com/dzerbino/velvet Description: Nucleic acid sequence assembler for very short reads, long version Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. . This package installs special long-mode versions of Velvet, as recommended in the Velvet tutorials. drwxr-xr-x root/root 0 2022-11-29 19:22 ./ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/bin/ -rwxr-xr-x root/root 190552 2022-11-29 19:22 ./usr/bin/velvetg_127 -rwxr-xr-x root/root 190552 2022-11-29 19:22 ./usr/bin/velvetg_127_long -rwxr-xr-x root/root 190552 2022-11-29 19:22 ./usr/bin/velvetg_63 -rwxr-xr-x root/root 190552 2022-11-29 19:22 ./usr/bin/velvetg_63_long -rwxr-xr-x root/root 190540 2022-11-29 19:22 ./usr/bin/velvetg_long -rwxr-xr-x root/root 63504 2022-11-29 19:22 ./usr/bin/velveth_127 -rwxr-xr-x root/root 63504 2022-11-29 19:22 ./usr/bin/velveth_127_long -rwxr-xr-x root/root 63504 2022-11-29 19:22 ./usr/bin/velveth_63 -rwxr-xr-x root/root 63504 2022-11-29 19:22 ./usr/bin/velveth_63_long -rwxr-xr-x root/root 63492 2022-11-29 19:22 ./usr/bin/velveth_long drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/doc/velvet-long/ -rw-r--r-- root/root 1013 2022-11-29 19:22 ./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 2022-11-29 19:22 ./usr/share/doc/velvet-long/copyright drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/man/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/man/man1/ -rw-r--r-- root/root 1488 2022-11-29 19:22 ./usr/share/man/man1/velvetg_127.1.gz -rw-r--r-- root/root 1508 2022-11-29 19:22 ./usr/share/man/man1/velvetg_127_long.1.gz -rw-r--r-- root/root 1487 2022-11-29 19:22 ./usr/share/man/man1/velvetg_63.1.gz -rw-r--r-- root/root 1507 2022-11-29 19:22 ./usr/share/man/man1/velvetg_63_long.1.gz -rw-r--r-- root/root 1483 2022-11-29 19:22 ./usr/share/man/man1/velvetg_long.1.gz -rw-r--r-- root/root 1442 2022-11-29 19:22 ./usr/share/man/man1/velveth_127.1.gz -rw-r--r-- root/root 1463 2022-11-29 19:22 ./usr/share/man/man1/velveth_127_long.1.gz -rw-r--r-- root/root 1441 2022-11-29 19:22 ./usr/share/man/man1/velveth_63.1.gz -rw-r--r-- root/root 1462 2022-11-29 19:22 ./usr/share/man/man1/velveth_63_long.1.gz -rw-r--r-- root/root 1454 2022-11-29 19:22 ./usr/share/man/man1/velveth_long.1.gz velvet_1.2.10+dfsg1-8_armhf.deb ------------------------------- new Debian package, version 2.0. size 640852 bytes: control archive=1332 bytes. 877 bytes, 19 lines control 1161 bytes, 18 lines md5sums Package: velvet Version: 1.2.10+dfsg1-8 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1055 Depends: libc6 (>= 2.34), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2) Suggests: velvet-example Section: science Priority: optional Homepage: https://github.com/dzerbino/velvet Description: Nucleic acid sequence assembler for very short reads Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. drwxr-xr-x root/root 0 2022-11-29 19:22 ./ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/bin/ -rwxr-xr-x root/root 190532 2022-11-29 19:22 ./usr/bin/velvetg -rwxr-xr-x root/root 190532 2022-11-29 19:22 ./usr/bin/velvetg_de -rwxr-xr-x root/root 63484 2022-11-29 19:22 ./usr/bin/velveth -rwxr-xr-x root/root 67580 2022-11-29 19:22 ./usr/bin/velveth_de drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/doc-base/ -rw-r--r-- root/root 243 2022-11-29 19:22 ./usr/share/doc-base/velvet.velvet drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./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 88580 2022-11-29 19:22 ./usr/share/doc/velvet/Columbus_manual.pdf -rw-r--r-- root/root 439986 2022-11-29 19:22 ./usr/share/doc/velvet/Manual.pdf -rw-r--r-- root/root 220 2022-11-29 19:22 ./usr/share/doc/velvet/README.Debian -rw-r--r-- root/root 405 2022-11-29 19:22 ./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 1010 2022-11-29 19:22 ./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 2022-11-29 19:22 ./usr/share/doc/velvet/copyright drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/man/ drwxr-xr-x root/root 0 2022-11-29 19:22 ./usr/share/man/man1/ -rw-r--r-- root/root 1460 2022-11-29 19:22 ./usr/share/man/man1/velvetg.1.gz -rw-r--r-- root/root 1479 2022-11-29 19:22 ./usr/share/man/man1/velvetg_de.1.gz -rw-r--r-- root/root 1422 2022-11-29 19:22 ./usr/share/man/man1/velveth.1.gz -rw-r--r-- root/root 1453 2022-11-29 19:22 ./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: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl 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-listing-perl libfont-ttf-perl 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 libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl 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 libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 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-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 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-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 liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl 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-listing-perl libfont-ttf-perl 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 libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl 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 libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 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-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 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:armhf unzip 0 upgraded, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 13.7 MB of archives. After this operation, 51.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.12-2 [1419 kB] Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB] Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.44.0-1 [881 kB] Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.15.0-1 [2906 kB] Get:13 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:15 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:18 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB] Get:24 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:26 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.21-1 [95.6 kB] Get:29 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:30 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.60-1 [219 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:32 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:33 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:34 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:35 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:36 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:37 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:38 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:39 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:40 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:41 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.37-1 [131 kB] Get:42 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:43 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:44 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:45 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:46 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.59-1 [43.6 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:49 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:50 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:51 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:55 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:56 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:57 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:58 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:59 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:60 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:61 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:62 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:63 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:64 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:65 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:69 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:70 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:71 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:72 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:73 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:74 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.084-1 [216 kB] Get:75 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:76 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.11-1 [10.5 kB] Get:77 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:78 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.72-1 [187 kB] Get:79 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:80 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:81 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:82 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:83 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:86 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:87 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-6 [37.8 kB] Get:88 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:89 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:91 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:92 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:93 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:94 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:95 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:96 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:97 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:98 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:99 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1 [12.5 kB] Get:100 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:101 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:102 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:103 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:104 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1 [43.0 kB] Get:105 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:106 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1 [99.5 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1 [102 kB] Get:108 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:109 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.38-1 [60.0 kB] Get:110 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-1 [28.8 kB] Get:111 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:113 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB] Get:114 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:115 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:116 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:117 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:118 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:119 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:120 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB] Get:121 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-6 [63.1 kB] Get:122 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:123 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:124 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:125 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.7 MB in 0s (81.1 MB/s) Selecting previously unselected package netbase. (Reading database ... 28982 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_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.12-2_amd64.deb ... Unpacking openssl (3.0.12-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../005-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../006-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package gpgconf. Preparing to unpack .../007-gpgconf_2.2.40-1.1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../008-libsqlite3-0_3.44.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.44.0-1) ... Selecting previously unselected package gpg. Preparing to unpack .../009-gpg_2.2.40-1.1_amd64.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../010-iso-codes_4.15.0-1_all.deb ... Unpacking iso-codes (4.15.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../011-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../012-libapt-pkg-perl_0.1.40+b2_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b1_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-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 .../018-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../021-libvariable-magic-perl_0.63-1+b1_amd64.deb ... Unpacking libvariable-magic-perl (0.63-1+b1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../022-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:amd64. Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b1_amd64.deb ... Unpacking libberkeleydb-perl:amd64 (0.64-2+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../025-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../026-liburi-perl_5.21-1_all.deb ... Unpacking liburi-perl (5.21-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../027-libhtml-parser-perl_3.81-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../028-libcgi-pm-perl_4.60-1_all.deb ... Unpacking libcgi-pm-perl (4.60-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../029-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../030-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../031-libclass-xsaccessor-perl_1.19-4+b1_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b1) ... Selecting previously unselected package libclone-perl:amd64. Preparing to unpack .../032-libclone-perl_0.46-1_amd64.deb ... Unpacking libclone-perl:amd64 (0.46-1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../033-libconfig-tiny-perl_2.30-1_all.deb ... Unpacking libconfig-tiny-perl (2.30-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../034-libparams-util-perl_1.102-2+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-2+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../035-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../036-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../037-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../038-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:amd64. Preparing to unpack .../039-libcpanel-json-xs-perl_4.37-1_amd64.deb ... Unpacking libcpanel-json-xs-perl:amd64 (4.37-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../040-libdevel-stacktrace-perl_2.0400-2_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-2) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../041-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../042-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 .../043-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 .../044-libdata-dpath-perl_0.59-1_all.deb ... Unpacking libdata-dpath-perl (0.59-1) ... Selecting previously unselected package libdata-messagepack-perl. Preparing to unpack .../045-libdata-messagepack-perl_1.02-1+b1_amd64.deb ... Unpacking libdata-messagepack-perl (1.02-1+b1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../046-libnet-domain-tld-perl_1.75-3_all.deb ... Unpacking libnet-domain-tld-perl (1.75-3) ... Selecting previously unselected package libdata-validate-domain-perl. Preparing to unpack .../047-libdata-validate-domain-perl_0.10-1.1_all.deb ... Unpacking libdata-validate-domain-perl (0.10-1.1) ... Selecting previously unselected package libnet-ipv6addr-perl. Preparing to unpack .../048-libnet-ipv6addr-perl_1.02-1_all.deb ... Unpacking libnet-ipv6addr-perl (1.02-1) ... Selecting previously unselected package libnet-netmask-perl. Preparing to unpack .../049-libnet-netmask-perl_2.0002-2_all.deb ... Unpacking libnet-netmask-perl (2.0002-2) ... Selecting previously unselected package libnetaddr-ip-perl. Preparing to unpack .../050-libnetaddr-ip-perl_4.079+dfsg-2+b1_amd64.deb ... Unpacking libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Selecting previously unselected package libdata-validate-ip-perl. Preparing to unpack .../051-libdata-validate-ip-perl_0.31-1_all.deb ... Unpacking libdata-validate-ip-perl (0.31-1) ... Selecting previously unselected package libdata-validate-uri-perl. Preparing to unpack .../052-libdata-validate-uri-perl_0.07-2_all.deb ... Unpacking libdata-validate-uri-perl (0.07-2) ... Selecting previously unselected package libdevel-size-perl. Preparing to unpack .../053-libdevel-size-perl_0.83-2+b1_amd64.deb ... Unpacking libdevel-size-perl (0.83-2+b1) ... Selecting previously unselected package libemail-address-xs-perl. Preparing to unpack .../054-libemail-address-xs-perl_1.05-1+b1_amd64.deb ... Unpacking libemail-address-xs-perl (1.05-1+b1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../055-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../056-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 .../057-libfile-basedir-perl_0.09-2_all.deb ... Unpacking libfile-basedir-perl (0.09-2) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../058-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../059-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../060-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libfont-ttf-perl. Preparing to unpack .../061-libfont-ttf-perl_1.06-2_all.deb ... Unpacking libfont-ttf-perl (1.06-2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../062-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../063-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../064-libhttp-message-perl_6.45-1_all.deb ... Unpacking libhttp-message-perl (6.45-1) ... Selecting previously unselected package libhtml-form-perl. Preparing to unpack .../065-libhtml-form-perl_6.11-1_all.deb ... Unpacking libhtml-form-perl (6.11-1) ... Selecting previously unselected package libhtml-html5-entities-perl. Preparing to unpack .../066-libhtml-html5-entities-perl_0.004-3_all.deb ... Unpacking libhtml-html5-entities-perl (0.004-3) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../067-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../068-libhttp-cookies-perl_6.10-1_all.deb ... Unpacking libhttp-cookies-perl (6.10-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../069-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../070-perl-openssl-defaults_7+b1_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (7+b1) ... Selecting previously unselected package libnet-ssleay-perl:amd64. Preparing to unpack .../071-libnet-ssleay-perl_1.92-2+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.92-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../072-libio-socket-ssl-perl_2.084-1_all.deb ... Unpacking libio-socket-ssl-perl (2.084-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../073-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../074-liblwp-protocol-https-perl_6.11-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.11-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../075-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../076-libwww-perl_6.72-1_all.deb ... Unpacking libwww-perl (6.72-1) ... Selecting previously unselected package libhtml-tokeparser-simple-perl. Preparing to unpack .../077-libhtml-tokeparser-simple-perl_3.16-4_all.deb ... Unpacking libhtml-tokeparser-simple-perl (3.16-4) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../078-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package libio-interactive-perl. Preparing to unpack .../079-libio-interactive-perl_1.025-1_all.deb ... Unpacking libio-interactive-perl (1.025-1) ... Selecting previously unselected package libipc-run3-perl. Preparing to unpack .../080-libipc-run3-perl_0.048-3_all.deb ... Unpacking libipc-run3-perl (0.048-3) ... Selecting previously unselected package libjson-maybexs-perl. Preparing to unpack .../081-libjson-maybexs-perl_1.004005-1_all.deb ... Unpacking libjson-maybexs-perl (1.004005-1) ... Selecting previously unselected package liblist-compare-perl. Preparing to unpack .../082-liblist-compare-perl_0.55-2_all.deb ... Unpacking liblist-compare-perl (0.55-2) ... Selecting previously unselected package liblist-someutils-perl. Preparing to unpack .../083-liblist-someutils-perl_0.59-1_all.deb ... Unpacking liblist-someutils-perl (0.59-1) ... Selecting previously unselected package liblist-utilsby-perl. Preparing to unpack .../084-liblist-utilsby-perl_0.12-2_all.deb ... Unpacking liblist-utilsby-perl (0.12-2) ... Selecting previously unselected package liblz1:amd64. Preparing to unpack .../085-liblz1_1.13-6_amd64.deb ... Unpacking liblz1:amd64 (1.13-6) ... Selecting previously unselected package liblzo2-2:amd64. Preparing to unpack .../086-liblzo2-2_2.10-2_amd64.deb ... Unpacking liblzo2-2:amd64 (2.10-2) ... Selecting previously unselected package libmarkdown2:amd64. Preparing to unpack .../087-libmarkdown2_2.2.7-2_amd64.deb ... Unpacking libmarkdown2:amd64 (2.2.7-2) ... Selecting previously unselected package libmldbm-perl. Preparing to unpack .../088-libmldbm-perl_2.05-4_all.deb ... Unpacking libmldbm-perl (2.05-4) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../089-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../090-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../091-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libstrictures-perl. Preparing to unpack .../092-libstrictures-perl_2.000006-1_all.deb ... Unpacking libstrictures-perl (2.000006-1) ... Selecting previously unselected package libmoox-aliases-perl. Preparing to unpack .../093-libmoox-aliases-perl_0.001006-2_all.deb ... Unpacking libmoox-aliases-perl (0.001006-2) ... Selecting previously unselected package libmouse-perl. Preparing to unpack .../094-libmouse-perl_2.5.10-1+b3_amd64.deb ... Unpacking libmouse-perl (2.5.10-1+b3) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../095-libpackage-stash-perl_0.40-1_all.deb ... Unpacking libpackage-stash-perl (0.40-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../096-libsub-identify-perl_0.14-3_amd64.deb ... Unpacking libsub-identify-perl (0.14-3) ... Selecting previously unselected package libsub-name-perl:amd64. Preparing to unpack .../097-libsub-name-perl_0.27-1_amd64.deb ... Unpacking libsub-name-perl:amd64 (0.27-1) ... Selecting previously unselected package libnamespace-clean-perl. Preparing to unpack .../098-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 .../099-libpath-tiny-perl_0.144-1_all.deb ... Unpacking libpath-tiny-perl (0.144-1) ... Selecting previously unselected package libperlio-gzip-perl. Preparing to unpack .../100-libperlio-gzip-perl_0.20-1+b1_amd64.deb ... Unpacking libperlio-gzip-perl (0.20-1+b1) ... Selecting previously unselected package libperlio-utf8-strict-perl. Preparing to unpack .../101-libperlio-utf8-strict-perl_0.010-1_amd64.deb ... Unpacking libperlio-utf8-strict-perl (0.010-1) ... Selecting previously unselected package libproc-processtable-perl:amd64. Preparing to unpack .../102-libproc-processtable-perl_0.636-1_amd64.deb ... Unpacking libproc-processtable-perl:amd64 (0.636-1) ... Selecting previously unselected package libregexp-wildcards-perl. Preparing to unpack .../103-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 .../104-libsereal-decoder-perl_5.004+ds-1_amd64.deb ... Unpacking libsereal-decoder-perl (5.004+ds-1) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../105-libsereal-encoder-perl_5.004+ds-1_amd64.deb ... Unpacking libsereal-encoder-perl (5.004+ds-1) ... Selecting previously unselected package libsort-versions-perl. Preparing to unpack .../106-libsort-versions-perl_1.62-3_all.deb ... Unpacking libsort-versions-perl (1.62-3) ... Selecting previously unselected package libxs-parse-keyword-perl. Preparing to unpack .../107-libxs-parse-keyword-perl_0.38-1_amd64.deb ... Unpacking libxs-parse-keyword-perl (0.38-1) ... Selecting previously unselected package libsyntax-keyword-try-perl. Preparing to unpack .../108-libsyntax-keyword-try-perl_0.29-1_amd64.deb ... Unpacking libsyntax-keyword-try-perl (0.29-1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../109-libterm-readkey-perl_2.38-2+b1_amd64.deb ... Unpacking libterm-readkey-perl (2.38-2+b1) ... Selecting previously unselected package libtext-levenshteinxs-perl. Preparing to unpack .../110-libtext-levenshteinxs-perl_0.03-5+b1_amd64.deb ... Unpacking libtext-levenshteinxs-perl (0.03-5+b1) ... Selecting previously unselected package libtext-markdown-discount-perl. Preparing to unpack .../111-libtext-markdown-discount-perl_0.16-1_amd64.deb ... Unpacking libtext-markdown-discount-perl (0.16-1) ... Selecting previously unselected package libtext-xslate-perl:amd64. Preparing to unpack .../112-libtext-xslate-perl_3.5.9-1+b2_amd64.deb ... Unpacking libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Selecting previously unselected package libtime-duration-perl. Preparing to unpack .../113-libtime-duration-perl_1.21-2_all.deb ... Unpacking libtime-duration-perl (1.21-2) ... Selecting previously unselected package libtime-moment-perl. Preparing to unpack .../114-libtime-moment-perl_0.44-2+b1_amd64.deb ... Unpacking libtime-moment-perl (0.44-2+b1) ... Selecting previously unselected package libunicode-utf8-perl. Preparing to unpack .../115-libunicode-utf8-perl_0.62-2_amd64.deb ... Unpacking libunicode-utf8-perl (0.62-2) ... Selecting previously unselected package libwww-mechanize-perl. Preparing to unpack .../116-libwww-mechanize-perl_2.17-1_all.deb ... Unpacking libwww-mechanize-perl (2.17-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../117-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package libyaml-libyaml-perl. Preparing to unpack .../118-libyaml-libyaml-perl_0.86+ds-1_amd64.deb ... Unpacking libyaml-libyaml-perl (0.86+ds-1) ... Selecting previously unselected package plzip. Preparing to unpack .../119-plzip_1.10-6_amd64.deb ... Unpacking plzip (1.10-6) ... Selecting previously unselected package lzop. Preparing to unpack .../120-lzop_1.04-2_amd64.deb ... Unpacking lzop (1.04-2) ... Selecting previously unselected package patchutils. Preparing to unpack .../121-patchutils_0.4.2-1_amd64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package unzip. Preparing to unpack .../122-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package lintian. Preparing to unpack .../123-lintian_2.116.3_all.deb ... Unpacking lintian (2.116.3) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:armhf. Preparing to unpack .../124-sbuild-build-depends-lintian-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b2) ... Setting up liblz1:amd64 (1.13-6) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ... Setting up plzip (1.10-6) ... 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 libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.37-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:amd64 (3.44.0-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.6-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1) ... 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 patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.38-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... 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) ... Setting up libsyntax-keyword-try-perl (0.29-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.636-1) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.12-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up readline-common (8.2-1.3) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.21-1) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... 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 libreadline8:amd64 (8.2-1.3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libio-socket-ssl-perl (2.084-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... 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 (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.60-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... 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 (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.72-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.11-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.37-12) ... Processing triggers for man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... 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: 77520 Build-Time: 78 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 42 Job: velvet_1.2.10+dfsg1-8 Lintian: pass Machine Architecture: amd64 Package: velvet Package-Time: 132 Source-Version: 1.2.10+dfsg1-8 Space: 77520 Status: successful Version: 1.2.10+dfsg1-8 -------------------------------------------------------------------------------- Finished at 2023-11-10T23:07:27Z Build needed 00:02:12, 77520k disk space