sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | velvet 1.2.10+dfsg1-7 (amd64) Sat, 01 Jan 2022 19:03:48 +0000 | +==============================================================================+ Package: velvet Version: 1.2.10+dfsg1-7 Source Version: 1.2.10+dfsg1-7 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-a982c99a-b911-4af4-a56c-3f648f8d7ad3' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-G7RGwr/resolver-MWQtVr' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [165 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main amd64 Packages [8863 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9415 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8726 kB] Fetched 27.2 MB in 7s (3802 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://mirror.einval.org/debian sid/main velvet 1.2.10+dfsg1-7 (dsc) [2274 B] Get:2 http://mirror.einval.org/debian sid/main velvet 1.2.10+dfsg1-7 (tar) [13.6 MB] Get:3 http://mirror.einval.org/debian sid/main velvet 1.2.10+dfsg1-7 (diff) [16.8 kB] Fetched 13.6 MB in 0s (54.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/velvet-G7RGwr/velvet-1.2.10+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-G7RGwr' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, texlive-latex-base, texlive-latex-recommended, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, texlive-latex-base, texlive-latex-recommended, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [433 B] Get:5 copy:/<>/apt_archive ./ Packages [522 B] Fetched 1912 B in 0s (43.8 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-11-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file fontconfig-config fonts-dejavu-core fonts-lmodern g++-11-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-11-base:amd64 gcc-11-cross-base gcc-11-x86-64-linux-gnu gcc-11-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbrotli1 libbsd0 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcairo2 libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfreetype6 libgcc-11-dev:amd64 libgcc-11-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libglib2.0-0 libgomp1:amd64 libgomp1-amd64-cross libgraphite2-3 libgssapi-krb5-2:amd64 libharfbuzz0b libice6 libicu67 libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkeyutils1:amd64 libkpathsea6 libkrb5-3:amd64 libkrb5support0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1 libmd0 libnsl-dev:amd64 libnsl2:amd64 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libptexenc1 libquadmath0:amd64 libquadmath0-amd64-cross libsigsegv2 libsm6 libssl1.1:amd64 libstdc++-11-dev:amd64 libstdc++-11-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64 libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-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:amd64 linux-libc-dev-amd64-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:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales cpp-doc dh-make binutils-multiarch g++-11-multilib-x86-64-linux-gnu gcc-11-doc gcc-11-multilib-x86-64-linux-gnu manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 krb5-doc:amd64 krb5-user:amd64 libstdc++-11-doc:amd64 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-latex-base-doc texlive-latex-recommended-doc texlive-luatex texlive-pstricks Recommended packages: curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales:amd64 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-x86-64-linux-gnu bsdextrautils cpp-11-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file fontconfig-config fonts-dejavu-core fonts-lmodern g++-11-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-11-base:amd64 gcc-11-cross-base gcc-11-x86-64-linux-gnu gcc-11-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbrotli1 libbsd0 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcairo2 libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfreetype6 libgcc-11-dev:amd64 libgcc-11-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libglib2.0-0 libgomp1:amd64 libgomp1-amd64-cross libgraphite2-3 libgssapi-krb5-2:amd64 libharfbuzz0b libice6 libicu67 libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkeyutils1:amd64 libkpathsea6 libkrb5-3:amd64 libkrb5support0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1 libmd0 libnsl-dev:amd64 libnsl2:amd64 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libptexenc1 libquadmath0:amd64 libquadmath0-amd64-cross libsigsegv2 libsm6 libssl1.1:amd64 libstdc++-11-dev:amd64 libstdc++-11-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64 libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-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:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 151 newly installed, 0 to remove and 0 not upgraded. Need to get 273 MB of archives. After this operation, 944 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [956 B] Get:2 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 tex-common all 6.17 [53.6 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.41-2 [295 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.41-2 [124 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.41-2 [66.8 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-8 [882 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.2-5 [144 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.4-2 [34.5 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-4 [1336 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1.1 [823 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 gcc-11-x86-64-linux-gnu-base arm64 11.2.0-9cross1 [205 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 cpp-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [48.2 MB] Get:23 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:11.2.0-2 [17.0 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.37-10 [2303 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-amd64-cross all 11.2.0-9cross1 [42.0 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libgomp1-amd64-cross all 11.2.0-9cross1 [104 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libitm1-amd64-cross all 11.2.0-9cross1 [25.5 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libatomic1-amd64-cross all 11.2.0-9cross1 [8764 B] Get:31 http://mirror.einval.org/debian sid/main arm64 libasan6-amd64-cross all 11.2.0-9cross1 [2044 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 liblsan0-amd64-cross all 11.2.0-9cross1 [885 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libtsan0-amd64-cross all 11.2.0-9cross1 [2010 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libc6-amd64-cross all 2.33-1cross1 [1579 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libstdc++6-amd64-cross all 11.2.0-9cross1 [535 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libubsan1-amd64-cross all 11.2.0-9cross1 [834 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libquadmath0-amd64-cross all 11.2.0-9cross1 [145 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libgcc-11-dev-amd64-cross all 11.2.0-9cross1 [2357 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 gcc-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [54.7 MB] Get:40 http://mirror.einval.org/debian sid/main arm64 gcc-x86-64-linux-gnu arm64 4:11.2.0-2 [1460 B] Get:41 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-amd64-cross all 5.15.5-1cross1 [1576 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libc6-dev-amd64-cross all 2.33-1cross1 [2272 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libstdc++-11-dev-amd64-cross all 11.2.0-9cross1 [1952 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 g++-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [52.2 MB] Get:45 http://mirror.einval.org/debian sid/main arm64 g++-x86-64-linux-gnu arm64 4:11.2.0-2 [1176 B] Get:46 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.12+dfsg-5+b1 [633 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B] Get:62 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.6 [193 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.186-1 [177 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.6 [1054 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 fonts-lmodern all 2.004.5-6.1 [4540 kB] Get:78 http://mirror.einval.org/debian sid/main amd64 gcc-11-base amd64 11.2.0-13 [207 kB] Get:79 http://mirror.einval.org/debian sid/main amd64 libgcc-s1 amd64 11.2.0-13 [42.0 kB] Get:80 http://mirror.einval.org/debian sid/main amd64 libc6 amd64 2.33-1 [2826 kB] Get:81 http://mirror.einval.org/debian sid/main amd64 libasan6 amd64 11.2.0-13 [2050 kB] Get:82 http://mirror.einval.org/debian sid/main amd64 libatomic1 amd64 11.2.0-13 [9048 B] Get:83 http://mirror.einval.org/debian sid/main arm64 libbrotli1 arm64 1.0.9-2+b3 [270 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libmd0 arm64 1.0.4-1 [29.5 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get:86 http://mirror.einval.org/debian sid/main amd64 linux-libc-dev amd64 5.15.5-2 [1457 kB] Get:87 http://mirror.einval.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.27-1 [89.0 kB] Get:88 http://mirror.einval.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.27-1 [104 kB] Get:89 http://mirror.einval.org/debian sid/main amd64 libcom-err2 amd64 1.46.5-1 [75.6 kB] Get:90 http://mirror.einval.org/debian sid/main amd64 libkrb5support0 amd64 1.18.3-7 [65.4 kB] Get:91 http://mirror.einval.org/debian sid/main amd64 libk5crypto3 amd64 1.18.3-7 [113 kB] Get:92 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:93 http://mirror.einval.org/debian sid/main amd64 libssl1.1 amd64 1.1.1m-1 [1557 kB] Get:94 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.18.3-7 [363 kB] Get:95 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.18.3-7 [165 kB] Get:96 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.2-2 [83.9 kB] Get:97 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:98 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:99 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:100 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.33-1 [2272 kB] Get:101 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.2-1 [90.1 kB] Get:102 http://mirror.einval.org/debian sid/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get:103 http://mirror.einval.org/debian sid/main arm64 libfreetype6 arm64 2.11.1+dfsg-1 [374 kB] Get:104 http://mirror.einval.org/debian sid/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get:105 http://mirror.einval.org/debian sid/main arm64 libpixman-1-0 arm64 0.40.0-1 [444 kB] Get:106 http://mirror.einval.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get:107 http://mirror.einval.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get:108 http://mirror.einval.org/debian sid/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get:109 http://mirror.einval.org/debian sid/main arm64 libx11-data all 2:1.7.2-2 [311 kB] Get:110 http://mirror.einval.org/debian sid/main arm64 libx11-6 arm64 2:1.7.2-2+b1 [751 kB] Get:111 http://mirror.einval.org/debian sid/main arm64 libxcb-render0 arm64 1.14-3 [111 kB] Get:112 http://mirror.einval.org/debian sid/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get:113 http://mirror.einval.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1 [51.6 kB] Get:114 http://mirror.einval.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get:115 http://mirror.einval.org/debian sid/main arm64 libcairo2 arm64 1.16.0-5 [648 kB] Get:116 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 11.2.0-13 [106 kB] Get:117 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 11.2.0-13 [26.0 kB] Get:118 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 11.2.0-13 [886 kB] Get:119 http://mirror.einval.org/debian sid/main amd64 libtsan0 amd64 11.2.0-13 [2019 kB] Get:120 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 11.2.0-13 [576 kB] Get:121 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 11.2.0-13 [835 kB] Get:122 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 11.2.0-13 [145 kB] Get:123 http://mirror.einval.org/debian sid/main amd64 libgcc-11-dev amd64 11.2.0-13 [2359 kB] Get:124 http://mirror.einval.org/debian sid/main arm64 libglib2.0-0 arm64 2.70.2-1 [1313 kB] Get:125 http://mirror.einval.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get:126 http://mirror.einval.org/debian sid/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get:127 http://mirror.einval.org/debian sid/main arm64 x11-common all 1:7.7+23 [252 kB] Get:128 http://mirror.einval.org/debian sid/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get:129 http://mirror.einval.org/debian sid/main arm64 libkpathsea6 arm64 2021.20210626.59705-1 [171 kB] Get:130 http://mirror.einval.org/debian sid/main arm64 libpaper1 arm64 1.1.28+b1 [21.4 kB] Get:131 http://mirror.einval.org/debian sid/main arm64 libpaper-utils arm64 1.1.28+b1 [18.3 kB] Get:132 http://mirror.einval.org/debian sid/main arm64 libptexenc1 arm64 2021.20210626.59705-1 [64.0 kB] Get:133 http://mirror.einval.org/debian sid/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get:134 http://mirror.einval.org/debian sid/main amd64 libstdc++-11-dev amd64 11.2.0-13 [1978 kB] Get:135 http://mirror.einval.org/debian sid/main arm64 libsynctex2 arm64 2021.20210626.59705-1 [77.6 kB] Get:136 http://mirror.einval.org/debian sid/main arm64 libteckit0 arm64 2.5.11+ds1-1 [299 kB] Get:137 http://mirror.einval.org/debian sid/main arm64 libtexlua53 arm64 2021.20210626.59705-1 [124 kB] Get:138 http://mirror.einval.org/debian sid/main arm64 libxt6 arm64 1:1.2.0-1 [176 kB] Get:139 http://mirror.einval.org/debian sid/main arm64 libxmu6 arm64 2:1.1.2-2+b3 [57.8 kB] Get:140 http://mirror.einval.org/debian sid/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB] Get:141 http://mirror.einval.org/debian sid/main arm64 libxaw7 arm64 2:1.0.13-1.1 [184 kB] Get:142 http://mirror.einval.org/debian sid/main arm64 libxi6 arm64 2:1.8-1 [82.1 kB] Get:143 http://mirror.einval.org/debian sid/main arm64 libzzip-0-13 arm64 0.13.72+dfsg.1-1.1 [58.3 kB] Get:144 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:145 http://mirror.einval.org/debian sid/main arm64 texlive-binaries arm64 2021.20210626.59705-1 [7734 kB] Get:146 http://mirror.einval.org/debian sid/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:147 http://mirror.einval.org/debian sid/main arm64 texlive-base all 2021.20211217-1 [21.1 MB] Get:148 http://mirror.einval.org/debian sid/main arm64 texlive-latex-base all 2021.20211217-1 [1159 kB] Get:149 http://mirror.einval.org/debian sid/main arm64 texlive-latex-recommended all 2021.20211217-1 [14.4 MB] Get:150 http://mirror.einval.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] Get:151 http://mirror.einval.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 273 MB in 3s (84.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12350 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package ucf. Preparing to unpack .../002-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package tex-common. Preparing to unpack .../003-tex-common_6.17_all.deb ... Unpacking tex-common (6.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.41-2_arm64.deb ... Unpacking libmagic-mgc (1:5.41-2) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../005-libmagic1_1%3a5.41-2_arm64.deb ... Unpacking libmagic1:arm64 (1:5.41-2) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.41-2_arm64.deb ... Unpacking file (1:5.41-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-8_arm64.deb ... Unpacking groff-base (1.22.4-8) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.37.2-5_arm64.deb ... Unpacking bsdextrautils (2.37.2-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.4-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.4-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.9.4-4_arm64.deb ... Unpacking man-db (2.9.4-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../013-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.1_all.deb ... Unpacking automake (1:1.16.5-1.1) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package gcc-11-x86-64-linux-gnu-base:arm64. Preparing to unpack .../019-gcc-11-x86-64-linux-gnu-base_11.2.0-9cross1_arm64.deb ... Unpacking gcc-11-x86-64-linux-gnu-base:arm64 (11.2.0-9cross1) ... Selecting previously unselected package cpp-11-x86-64-linux-gnu. Preparing to unpack .../020-cpp-11-x86-64-linux-gnu_11.2.0-9cross1_arm64.deb ... Unpacking cpp-11-x86-64-linux-gnu (11.2.0-9cross1) ... Selecting previously unselected package cpp-x86-64-linux-gnu. Preparing to unpack .../021-cpp-x86-64-linux-gnu_4%3a11.2.0-2_arm64.deb ... Unpacking cpp-x86-64-linux-gnu (4:11.2.0-2) ... Selecting previously unselected package cross-config. Preparing to unpack .../022-cross-config_2.6.18+nmu2_all.deb ... Unpacking cross-config (2.6.18+nmu2) ... Selecting previously unselected package binutils-x86-64-linux-gnu. Preparing to unpack .../023-binutils-x86-64-linux-gnu_2.37-10_arm64.deb ... Unpacking binutils-x86-64-linux-gnu (2.37-10) ... Selecting previously unselected package gcc-11-cross-base. Preparing to unpack .../024-gcc-11-cross-base_11.2.0-9cross1_all.deb ... Unpacking gcc-11-cross-base (11.2.0-9cross1) ... Selecting previously unselected package libgcc-s1-amd64-cross. Preparing to unpack .../025-libgcc-s1-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libgcc-s1-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libgomp1-amd64-cross. Preparing to unpack .../026-libgomp1-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libgomp1-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libitm1-amd64-cross. Preparing to unpack .../027-libitm1-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libitm1-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libatomic1-amd64-cross. Preparing to unpack .../028-libatomic1-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libatomic1-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libasan6-amd64-cross. Preparing to unpack .../029-libasan6-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libasan6-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package liblsan0-amd64-cross. Preparing to unpack .../030-liblsan0-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking liblsan0-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libtsan0-amd64-cross. Preparing to unpack .../031-libtsan0-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libtsan0-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libc6-amd64-cross. Preparing to unpack .../032-libc6-amd64-cross_2.33-1cross1_all.deb ... Unpacking libc6-amd64-cross (2.33-1cross1) ... Selecting previously unselected package libstdc++6-amd64-cross. Preparing to unpack .../033-libstdc++6-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libstdc++6-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libubsan1-amd64-cross. Preparing to unpack .../034-libubsan1-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libubsan1-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libquadmath0-amd64-cross. Preparing to unpack .../035-libquadmath0-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libquadmath0-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package libgcc-11-dev-amd64-cross. Preparing to unpack .../036-libgcc-11-dev-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libgcc-11-dev-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package gcc-11-x86-64-linux-gnu. Preparing to unpack .../037-gcc-11-x86-64-linux-gnu_11.2.0-9cross1_arm64.deb ... Unpacking gcc-11-x86-64-linux-gnu (11.2.0-9cross1) ... Selecting previously unselected package gcc-x86-64-linux-gnu. Preparing to unpack .../038-gcc-x86-64-linux-gnu_4%3a11.2.0-2_arm64.deb ... Unpacking gcc-x86-64-linux-gnu (4:11.2.0-2) ... Selecting previously unselected package linux-libc-dev-amd64-cross. Preparing to unpack .../039-linux-libc-dev-amd64-cross_5.15.5-1cross1_all.deb ... Unpacking linux-libc-dev-amd64-cross (5.15.5-1cross1) ... Selecting previously unselected package libc6-dev-amd64-cross. Preparing to unpack .../040-libc6-dev-amd64-cross_2.33-1cross1_all.deb ... Unpacking libc6-dev-amd64-cross (2.33-1cross1) ... Selecting previously unselected package libstdc++-11-dev-amd64-cross. Preparing to unpack .../041-libstdc++-11-dev-amd64-cross_11.2.0-9cross1_all.deb ... Unpacking libstdc++-11-dev-amd64-cross (11.2.0-9cross1) ... Selecting previously unselected package g++-11-x86-64-linux-gnu. Preparing to unpack .../042-g++-11-x86-64-linux-gnu_11.2.0-9cross1_arm64.deb ... Unpacking g++-11-x86-64-linux-gnu (11.2.0-9cross1) ... Selecting previously unselected package g++-x86-64-linux-gnu. Preparing to unpack .../043-g++-x86-64-linux-gnu_4%3a11.2.0-2_arm64.deb ... Unpacking g++-x86-64-linux-gnu (4:11.2.0-2) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../044-libconfig-inifiles-perl_3.000003-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../045-libio-string-perl_1.08-3.1_all.deb ... Unpacking libio-string-perl (1.08-3.1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../046-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../047-libxml2_2.9.12+dfsg-5+b1_arm64.deb ... Unpacking libxml2:arm64 (2.9.12+dfsg-5+b1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../048-libxml-namespacesupport-perl_1.12-1.1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1.1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../049-libxml-sax-base-perl_1.09-1.1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1.1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../050-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 .../051-libxml-libxml-perl_2.0134+dfsg-2+b1_arm64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-2+b1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../052-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../053-libyaml-perl_1.30-1_all.deb ... Unpacking libyaml-perl (1.30-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../054-libconfig-auto-perl_0.44-1.1_all.deb ... Unpacking libconfig-auto-perl (0.44-1.1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../055-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../056-libfile-homedir-perl_1.006-1_all.deb ... Unpacking libfile-homedir-perl (1.006-1) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../057-libdebian-dpkgcross-perl_2.6.18+nmu2_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.18+nmu2) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../058-dpkg-cross_2.6.18+nmu2_all.deb ... Unpacking dpkg-cross (2.6.18+nmu2) ... Selecting previously unselected package crossbuild-essential-amd64. Preparing to unpack .../059-crossbuild-essential-amd64_12.9_all.deb ... Unpacking crossbuild-essential-amd64 (12.9) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../060-libdebhelper-perl_13.6_all.deb ... Unpacking libdebhelper-perl (13.6) ... Selecting previously unselected package libtool. Preparing to unpack .../061-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../062-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../063-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 .../064-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../065-libfile-stripnondeterminism-perl_1.13.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../066-dh-strip-nondeterminism_1.13.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../067-libelf1_0.186-1_arm64.deb ... Unpacking libelf1:arm64 (0.186-1) ... Selecting previously unselected package dwz. Preparing to unpack .../068-dwz_0.14-1_arm64.deb ... Unpacking dwz (0.14-1) ... Selecting previously unselected package gettext. Preparing to unpack .../069-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../070-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../071-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. 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Setting up libgomp1-amd64-cross (11.2.0-9cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libitm1-amd64-cross (11.2.0-9cross1) ... Setting up libptexenc1:arm64 (2021.20210626.59705-1) ... Setting up libatomic1-amd64-cross (11.2.0-9cross1) ... Setting up libfreetype6:arm64 (2.11.1+dfsg-1) ... Setting up libquadmath0-amd64-cross (11.2.0-9cross1) ... Setting up libubsan1-amd64-cross (11.2.0-9cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-8) ... Setting up libx11-6:arm64 (2:1.7.2-2+b1) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up cpp-x86-64-linux-gnu (4:11.2.0-2) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgcc-11-dev-amd64-cross (11.2.0-9cross1) ... Setting up libpaper1:arm64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.4-1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-4) ... 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 dh-autoreconf (20) ... Setting up tex-common (6.17) ... update-language: texlive-base not installed and configured, doing nothing! Setting up gcc-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+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 libstdc++-11-dev-amd64-cross (11.2.0-9cross1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up g++-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up libxmu6:arm64 (2:1.1.2-2+b3) ... Setting up libxi6:arm64 (2:1.8-1) ... Setting up gcc-x86-64-linux-gnu (4:11.2.0-2) ... Setting up debhelper (13.6) ... Setting up libxaw7:arm64 (2:1.0.13-1.1) ... Setting up libcairo2:arm64 (1.16.0-5) ... Setting up libxml-simple-perl (2.25-1) ... Setting up texlive-binaries (2021.20210626.59705-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up g++-x86-64-linux-gnu (4:11.2.0-2) ... Setting up texlive-base (2021.20211217-1) ... /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. 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 libconfig-auto-perl (0.44-1.1) ... Setting up texlive-latex-base (2021.20211217-1) ... Setting up texlive-latex-recommended (2021.20211217-1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-amd64 (12.9) ... Setting up libgcc-s1:amd64 (11.2.0-13) ... Setting up libc6:amd64 (2.33-1) ... Setting up libstdc++6:amd64 (11.2.0-13) ... Setting up liblsan0:amd64 (11.2.0-13) ... Setting up libitm1:amd64 (11.2.0-13) ... Setting up libtsan0:amd64 (11.2.0-13) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libssl1.1:amd64 (1.1.1m-1) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Setting up libcrypt1:amd64 (1:4.4.27-1) ... Setting up libcom-err2:amd64 (1.46.5-1) ... Setting up libgomp1:amd64 (11.2.0-13) ... Setting up libasan6:amd64 (11.2.0-13) ... Setting up libkrb5support0:amd64 (1.18.3-7) ... Setting up libquadmath0:amd64 (11.2.0-13) ... Setting up libatomic1:amd64 (11.2.0-13) ... Setting up libk5crypto3:amd64 (1.18.3-7) ... Setting up libubsan1:amd64 (11.2.0-13) ... Setting up libgcc-11-dev:amd64 (11.2.0-13) ... Setting up libcrypt-dev:amd64 (1:4.4.27-1) ... Setting up libkrb5-3:amd64 (1.18.3-7) ... Setting up libgssapi-krb5-2:amd64 (1.18.3-7) ... Setting up libtirpc3:amd64 (1.3.2-2) ... Setting up libtirpc-dev:amd64 (1.3.2-2) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.33-1) ... Setting up libstdc++-11-dev:amd64 (11.2.0-13) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.33-1) ... Processing triggers for tex-common (6.17) ... 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 (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.37-10 dpkg-dev_1.21.1 g++-11_11.2.0-13 gcc-11_11.2.0-13 libc6-dev_2.33-1 libstdc++-11-dev_11.2.0-13 libstdc++-11-dev-amd64-cross_11.2.0-9cross1 libstdc++6_11.2.0-13 libstdc++6-amd64-cross_11.2.0-9cross1 linux-libc-dev_5.15.5-2 Package versions: adduser_3.118 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-5+b1 binutils_2.37-10 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: velvet Binary: velvet, velvet-long, velvet-example, velvet-tests Architecture: any all Version: 1.2.10+dfsg1-7 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~zerbino/velvet/ Standards-Version: 4.4.1 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 (= 12), 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 af5df03fcc81849fccef3d7aada178ff931a3b40 16832 velvet_1.2.10+dfsg1-7.debian.tar.xz Checksums-Sha256: 368d760ad56ffa010a2ae72b25d46680ecb7ad8cc573cf6c389848c87b32ee26 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 478f6db97a946075c949655012e60767041b524808b85922c3feef1ef768f316 16832 velvet_1.2.10+dfsg1-7.debian.tar.xz Files: 7a58a6d75cdc8b89d1c605033050bbcf 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 7cfa57445205ef35873e4b7c30d50f07 16832 velvet_1.2.10+dfsg1-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl3sDf8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGMRA/+McLdXfGg7CTd6R8Fs/CzRacsgGSmkvWH gQZIIrJUshhWcTfaHY4Nts4MX3s3UpfmM2HmqFnCq0DMdikv1AeVctZ9oj3bIkuS HYJOFePjEHywlr5C1RZFMCM11+kHAynKBBHuGVl+D/kDkbqHG6RYP3OXUp93c+SD zasazCoCPSpxUZ8bVgH1i7sW4cQjKx8AsTm31FrwNOBdmVYLkcRjCi0eFVXuJxRT l89eDs29CiKD01m7cdV6UdYLo/TID6RR4K+UE+Uy75HRBPQontm+o6D4c4vNBzJw W5lCU3Ky/WDIJH+eNx1uxODiPv4EJioLjBWwiUad6kvheEzPz2MN+ulhPzft9Yn7 Lcy1WYpJpGl8TMGmSbD2i+FtFcH/sdTO0ciIy7Dz5h8Izh3DK8JiqLwSYrINyoPG gpb7+UsknpIRIz9AD6YZrC1Zrfo/4yaRx1YdBZkwxM6/LHVtCm5UCjTU5zGLvev2 q5NtWRoaJEtyriQnM7JkJEO6N5TjuZ3mYRrJMiNT4uIcaDdELelX/ps7DCidZk9/ V7zyEQmGjsMF/obHHj82eFLayiwUmVU0CumV7R92tvFlv3o8zuXz5XiI/cJmE1ov 5NULZACFUt/k00u/muwckMCJhEgdZi/o+e9zZqQRwuZs7eY9sQkwkboNteBHX+pO SJ8TagYJ4TI= =4/km -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.DHiY1kF9/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 7 20:39:27 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./velvet_1.2.10+dfsg1-7.dsc 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+dfsg1-7.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 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-a982c99a-b911-4af4-a56c-3f648f8d7ad3 SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build-arch dh build-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 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-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 -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 x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>' mv velveth velveth_long ; mv velvetg velvetg_long #Make _63 kmer version dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>' mv velveth velveth_63 ; mv velvetg velvetg_63 #And also one with both options dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-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 -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 x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>' mv velveth velveth_63_long ; mv velvetg velvetg_63_long #Make _127 kmer version dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>' mv velveth velveth_127 ; mv velvetg velvetg_127 #And also one with both options dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-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 -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 x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>' mv velveth velveth_127_long ; mv velvetg velvetg_127_long touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2021-11-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 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/generic/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/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.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/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/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/latexconfig/epstopdf-sys.cfg)) [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 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on Manual.pdf (21 pages, 432064 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2021-11-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 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/generic/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/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (./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/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) Output written on Manual.pdf (22 pages, 439974 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2021-11-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 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 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 88585 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 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o 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; | ^ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:29: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:15: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value [-Waddress-of-packed-member] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --no-parallel dh_testroot -a dh_prep -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install # remove extra copies of GPL find /<>/debian -type f -name 'LICENSE*' -delete #MetaVelvet should be scrubbed, and VelvetOptimiser is now separate. Note that these #will not have been installed if this was a binarry-only build. [ ! -e debian/velvet-example/usr ] || \ cp debian/VelvetOptimiser.README debian/velvet-example/usr/share/doc/velvet/contrib/ make[1]: Leaving directory '/<>' 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+dfsg1-7_amd64.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-7_amd64.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb'. dpkg-genbuildinfo --build=any -O../velvet_1.2.10+dfsg1-7_amd64.buildinfo dpkg-genchanges --build=any -O../velvet_1.2.10+dfsg1-7_amd64.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 2022-01-01T19:10:40Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ velvet_1.2.10+dfsg1-7_amd64.changes: ------------------------------------ Format: 1.8 Date: Sat, 07 Dec 2019 21:28:03 +0100 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 1.2.10+dfsg1-7 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 Closes: 929563 Changes: velvet (1.2.10+dfsg1-7) unstable; urgency=medium . * velvet-examples: Depends: velvet-tests Closes: #929563 Checksums-Sha1: 274156bc823baacbc9f810ac4a0d197b27bacd9d 964592 velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb 3bfd93c75623741b66327c6ea7f65d482b5b5969 1902268 velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb b98c94db29c92dbd8d4c44db1c1ae501d18be4b8 210904 velvet-long_1.2.10+dfsg1-7_amd64.deb fb88fcf94bfb9bd19beb5c1fca7a1b41eb4b5a6d 6927 velvet_1.2.10+dfsg1-7_amd64.buildinfo 652baffbd5cbba60a826e808d4a85cb667a69859 661384 velvet_1.2.10+dfsg1-7_amd64.deb Checksums-Sha256: 541e6f44ad3af885f78701aa125d6990e805a99b4affe07f8f51ab7c404fd9a5 964592 velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb 62f5fa8c40a2b9e58f3aeff8bac9fc579e2e044b6ae56284caf886ded6c39c8c 1902268 velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb ec1180c8405d087379e6a191514af1226ff0c63153df9a38e3720a2949739957 210904 velvet-long_1.2.10+dfsg1-7_amd64.deb c498c5361887b20451494448dd7a598178546eb62b714804eda537bba7499363 6927 velvet_1.2.10+dfsg1-7_amd64.buildinfo 6ef13d8e89bfafa2af9d8a7aa4d6a1f707440eadc10738ce413b35e0562f2098 661384 velvet_1.2.10+dfsg1-7_amd64.deb Files: 31f2f2abc4f8bda2074bc9d5fd32e7da 964592 debug optional velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb a82b0dd590111c50456cf220d25ab64c 1902268 debug optional velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb 0d816062652de4e0461cebc2e762ae17 210904 science optional velvet-long_1.2.10+dfsg1-7_amd64.deb fcc90ebe7a0e9bb696da23b0df46184b 6927 science optional velvet_1.2.10+dfsg1-7_amd64.buildinfo ce6a0b56a35a565e8f87804f11dc57c6 661384 science optional velvet_1.2.10+dfsg1-7_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Architecture: amd64 Version: 1.2.10+dfsg1-7 Checksums-Md5: 31f2f2abc4f8bda2074bc9d5fd32e7da 964592 velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb a82b0dd590111c50456cf220d25ab64c 1902268 velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb 0d816062652de4e0461cebc2e762ae17 210904 velvet-long_1.2.10+dfsg1-7_amd64.deb ce6a0b56a35a565e8f87804f11dc57c6 661384 velvet_1.2.10+dfsg1-7_amd64.deb Checksums-Sha1: 274156bc823baacbc9f810ac4a0d197b27bacd9d 964592 velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb 3bfd93c75623741b66327c6ea7f65d482b5b5969 1902268 velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb b98c94db29c92dbd8d4c44db1c1ae501d18be4b8 210904 velvet-long_1.2.10+dfsg1-7_amd64.deb 652baffbd5cbba60a826e808d4a85cb667a69859 661384 velvet_1.2.10+dfsg1-7_amd64.deb Checksums-Sha256: 541e6f44ad3af885f78701aa125d6990e805a99b4affe07f8f51ab7c404fd9a5 964592 velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb 62f5fa8c40a2b9e58f3aeff8bac9fc579e2e044b6ae56284caf886ded6c39c8c 1902268 velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb ec1180c8405d087379e6a191514af1226ff0c63153df9a38e3720a2949739957 210904 velvet-long_1.2.10+dfsg1-7_amd64.deb 6ef13d8e89bfafa2af9d8a7aa4d6a1f707440eadc10738ce413b35e0562f2098 661384 velvet_1.2.10+dfsg1-7_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Sat, 01 Jan 2022 19:10:39 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 12), base-passwd (= 3.5.52), bash (= 5.1-5+b1), binutils (= 2.37-10), binutils-aarch64-linux-gnu (= 2.37-10), binutils-common (= 2.37-10), bsdextrautils (= 2.37.2-5), bsdutils (= 1:2.37.2-5), build-essential (= 12.9), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-13), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.6), debianutils (= 5.5-1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.7-5), dpkg (= 1.21.1), dpkg-dev (= 1.21.1), dwz (= 0.14-1), file (= 1:5.41-2), findutils (= 4.8.0-1), fontconfig-config (= 2.13.1-4.2), fonts-dejavu-core (= 2.37-2), fonts-lmodern (= 2.004.5-6.1), g++ (= 4:11.2.0-2), g++-11 (= 11.2.0-13), gcc (= 4:11.2.0-2), gcc-11 (= 11.2.0-13), gcc-11-base (= 11.2.0-13), gettext (= 0.21-4), gettext-base (= 0.21-4), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.10-4), hostname (= 3.23), init-system-helpers (= 1.61), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-13), libatomic1 (= 11.2.0-13), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.6-1), libaudit1 (= 1:3.0.6-1+b1), libbinutils (= 2.37-10), libblkid1 (= 2.37.2-5), libbrotli1 (= 1.0.9-2+b3), libbsd0 (= 0.11.3-1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.33-1), libc-dev-bin (= 2.33-1), libc6 (= 2.33-1), libc6-dev (= 2.33-1), libcairo2 (= 1.16.0-5), libcap-ng0 (= 0.7.9-2.2+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 11.2.0-13), libcom-err2 (= 1.46.5-1), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.37-10), libctf0 (= 2.37-10), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.261), libdebhelper-perl (= 13.6), libdpkg-perl (= 1.21.1), libelf1 (= 0.186-1), libexpat1 (= 2.4.2-1), libffi8 (= 3.4.2-3), libfile-stripnondeterminism-perl (= 1.13.0-1), libfontconfig1 (= 2.13.1-4.2), libfreetype6 (= 2.11.1+dfsg-1), libgcc-11-dev (= 11.2.0-13), libgcc-s1 (= 11.2.0-13), libgcrypt20 (= 1.9.4-5), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libglib2.0-0 (= 2.70.2-1), libgmp10 (= 2:6.2.1+dfsg-3), libgomp1 (= 11.2.0-13), libgpg-error0 (= 1.43-1), libgraphite2-3 (= 1.3.14-1), libgssapi-krb5-2 (= 1.18.3-7), libharfbuzz0b (= 2.7.4-1), libice6 (= 2:1.0.10-1), libicu67 (= 67.1-7), libisl23 (= 0.24-2), libitm1 (= 11.2.0-13), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2), libkpathsea6 (= 2021.20210626.59705-1), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), liblsan0 (= 11.2.0-13), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmd0 (= 1.0.4-1), libmount1 (= 2.37.2-5), libmpc3 (= 1.2.1-1), libmpfr6 (= 4.1.0-3), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libpam-modules (= 1.4.0-11), libpam-modules-bin (= 1.4.0-11), libpam-runtime (= 1.4.0-11), libpam0g (= 1.4.0-11), libpaper-utils (= 1.1.28+b1), libpaper1 (= 1.1.28+b1), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-6), libpipeline1 (= 1.5.4-2), libpixman-1-0 (= 0.40.0-1), libpng16-16 (= 1.6.37-3), libptexenc1 (= 2021.20210626.59705-1), libquadmath0 (= 11.2.0-13), libseccomp2 (= 2.5.3-2), libselinux1 (= 3.3-1+b1), libsigsegv2 (= 2.13-1), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.37.2-5), libssl1.1 (= 1.1.1m-1), libstdc++-11-dev (= 11.2.0-13), libstdc++6 (= 11.2.0-13), libsub-override-perl (= 0.09-2), libsynctex2 (= 2021.20210626.59705-1), libsystemd0 (= 249.7-1), libteckit0 (= 2.5.11+ds1-1), libtexlua53 (= 2021.20210626.59705-1), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15), libtsan0 (= 11.2.0-13), libubsan1 (= 11.2.0-13), libuchardet0 (= 0.0.7-1), libudev1 (= 249.7-1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-5), libx11-6 (= 2:1.7.2-2+b1), libx11-data (= 2:1.7.2-2), libxau6 (= 1:1.0.9-1), libxaw7 (= 2:1.0.13-1.1), libxcb-render0 (= 1.14-3), libxcb-shm0 (= 1.14-3), libxcb1 (= 1.14-3), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.4-1), libxi6 (= 2:1.8-1), libxml2 (= 2.9.12+dfsg-5+b1), libxmu6 (= 2:1.1.2-2+b3), libxpm4 (= 1:3.5.12-1), libxrender1 (= 1:0.9.10-1), libxt6 (= 1:1.2.0-1), libzstd1 (= 1.4.8+dfsg-3), libzzip-0-13 (= 0.13.72+dfsg.1-1.1), linux-libc-dev (= 5.15.5-2), login (= 1:4.8.1-2), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.9.4-4), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), patch (= 2.7.6-7), perl (= 5.32.1-6), perl-base (= 5.32.1-6), perl-modules-5.32 (= 5.32.1-6), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1), t1utils (= 1.41-4), tar (= 1.34+dfsg-1), tex-common (= 6.17), texlive-base (= 2021.20211217-1), texlive-binaries (= 2021.20210626.59705-1), texlive-latex-base (= 2021.20211217-1), texlive-latex-recommended (= 2021.20211217-1), ucf (= 3.0043), util-linux (= 2.37.2-5), x11-common (= 1:7.7+23), xdg-utils (= 1.1.3-4.1), xz-utils (= 5.2.5-2), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1575750483" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ velvet-dbgsym_1.2.10+dfsg1-7_amd64.deb -------------------------------------- new Debian package, version 2.0. size 964592 bytes: control archive=744 bytes. 504 bytes, 12 lines control 507 bytes, 5 lines md5sums Package: velvet-dbgsym Source: velvet Version: 1.2.10+dfsg1-7 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1054 Depends: velvet (= 1.2.10+dfsg1-7) Section: debug Priority: optional Description: debug symbols for velvet Build-Ids: 385f960fc341dbf8010f5d34afde5b849f32f4fa 54217a1a6a3c4d850a918499c5d1c81ad37ba5d4 7224e123fd3bdd3d2218d5b85da74bcfaaf4355b b1dff95ed492e878011aaf6bd45885654549e840 drwxr-xr-x root/root 0 2019-12-07 20:28 ./ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/lib/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/lib/debug/.build-id/38/ -rw-r--r-- root/root 405752 2019-12-07 20:28 ./usr/lib/debug/.build-id/38/5f960fc341dbf8010f5d34afde5b849f32f4fa.debug drwxr-xr-x root/root 0 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velvet-long-dbgsym_1.2.10+dfsg1-7_amd64.deb ------------------------------------------- new Debian package, version 2.0. size 1902268 bytes: control archive=1056 bytes. 765 bytes, 12 lines control 1148 bytes, 11 lines md5sums Package: velvet-long-dbgsym Source: velvet Version: 1.2.10+dfsg1-7 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2547 Depends: velvet-long (= 1.2.10+dfsg1-7) Section: debug Priority: optional Description: debug symbols for velvet-long Build-Ids: 08fd64b0129ba6e1a9ff48e2580a6d39da85c626 0c824f8fd3ad3237fc6e6fecb45ca697cacda656 0f6632257f381c88c480d2c4132472f583ebee5d 2623b296298bf3e1893a12a9294382dc6c543ad9 2691d0fa43db83c7cca34c7595005a6b41c88111 278ab71ee2098032d9f653a73d87f3b684f4f09c 282fa3e1ce38660efd39212760cc30044e963926 538efc290e0a167cb2b124909f236cbd9d4369a9 98c170275ed2df509cc578f20860e814daebbb7c d4bb4bd91dbef4461198adb70d298402038f4191 drwxr-xr-x root/root 0 2019-12-07 20:28 ./ drwxr-xr-x 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./usr/lib/debug/.build-id/d4/bb4bd91dbef4461198adb70d298402038f4191.debug drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 44088 2019-12-07 20:28 ./usr/lib/debug/.dwz/x86_64-linux-gnu/velvet-long.debug drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-12-07 20:28 ./usr/share/doc/velvet-long-dbgsym -> velvet-long velvet-long_1.2.10+dfsg1-7_amd64.deb ------------------------------------ new Debian package, version 2.0. size 210904 bytes: control archive=1460 bytes. 1003 bytes, 22 lines control 1499 bytes, 23 lines md5sums Package: velvet-long Source: velvet Version: 1.2.10+dfsg1-7 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1840 Depends: libc6 (>= 2.29), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2), velvet Section: science Priority: optional Homepage: https://www.ebi.ac.uk/~zerbino/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 2019-12-07 20:28 ./ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/bin/ -rwxr-xr-x root/root 273536 2019-12-07 20:28 ./usr/bin/velvetg_127 -rwxr-xr-x root/root 273536 2019-12-07 20:28 ./usr/bin/velvetg_127_long -rwxr-xr-x root/root 273536 2019-12-07 20:28 ./usr/bin/velvetg_63 -rwxr-xr-x root/root 273536 2019-12-07 20:28 ./usr/bin/velvetg_63_long -rwxr-xr-x root/root 273520 2019-12-07 20:28 ./usr/bin/velvetg_long -rwxr-xr-x root/root 93248 2019-12-07 20:28 ./usr/bin/velveth_127 -rwxr-xr-x root/root 93248 2019-12-07 20:28 ./usr/bin/velveth_127_long -rwxr-xr-x root/root 93248 2019-12-07 20:28 ./usr/bin/velveth_63 -rwxr-xr-x root/root 93248 2019-12-07 20:28 ./usr/bin/velveth_63_long -rwxr-xr-x root/root 89136 2019-12-07 20:28 ./usr/bin/velveth_long drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/doc/velvet-long/ -rw-r--r-- root/root 5118 2019-12-07 20:28 ./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 2019-12-07 20:28 ./usr/share/doc/velvet-long/copyright drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/man/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/man/man1/ -rw-r--r-- root/root 1488 2019-12-07 20:28 ./usr/share/man/man1/velvetg_127.1.gz -rw-r--r-- root/root 1508 2019-12-07 20:28 ./usr/share/man/man1/velvetg_127_long.1.gz -rw-r--r-- root/root 1487 2019-12-07 20:28 ./usr/share/man/man1/velvetg_63.1.gz -rw-r--r-- root/root 1507 2019-12-07 20:28 ./usr/share/man/man1/velvetg_63_long.1.gz -rw-r--r-- root/root 1483 2019-12-07 20:28 ./usr/share/man/man1/velvetg_long.1.gz -rw-r--r-- root/root 1442 2019-12-07 20:28 ./usr/share/man/man1/velveth_127.1.gz -rw-r--r-- root/root 1463 2019-12-07 20:28 ./usr/share/man/man1/velveth_127_long.1.gz -rw-r--r-- root/root 1441 2019-12-07 20:28 ./usr/share/man/man1/velveth_63.1.gz -rw-r--r-- root/root 1462 2019-12-07 20:28 ./usr/share/man/man1/velveth_63_long.1.gz -rw-r--r-- root/root 1454 2019-12-07 20:28 ./usr/share/man/man1/velveth_long.1.gz velvet_1.2.10+dfsg1-7_amd64.deb ------------------------------- new Debian package, version 2.0. size 661384 bytes: control archive=1332 bytes. 881 bytes, 19 lines control 1161 bytes, 18 lines md5sums Package: velvet Version: 1.2.10+dfsg1-7 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1273 Depends: libc6 (>= 2.29), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2) Suggests: velvet-example Section: science Priority: optional Homepage: https://www.ebi.ac.uk/~zerbino/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 2019-12-07 20:28 ./ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/bin/ -rwxr-xr-x root/root 273520 2019-12-07 20:28 ./usr/bin/velvetg -rwxr-xr-x root/root 273520 2019-12-07 20:28 ./usr/bin/velvetg_de -rwxr-xr-x root/root 89136 2019-12-07 20:28 ./usr/bin/velveth -rwxr-xr-x root/root 93240 2019-12-07 20:28 ./usr/bin/velveth_de drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/doc-base/ -rw-r--r-- root/root 243 2019-12-07 20:28 ./usr/share/doc-base/velvet.velvet drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./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 88585 2019-12-07 20:28 ./usr/share/doc/velvet/Columbus_manual.pdf -rw-r--r-- root/root 439974 2019-12-07 20:28 ./usr/share/doc/velvet/Manual.pdf -rw-r--r-- root/root 220 2019-12-07 20:28 ./usr/share/doc/velvet/README.Debian -rw-r--r-- root/root 405 2019-12-07 20:28 ./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 5118 2019-12-07 20:28 ./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 2019-12-07 20:28 ./usr/share/doc/velvet/copyright drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/man/ drwxr-xr-x root/root 0 2019-12-07 20:28 ./usr/share/man/man1/ -rw-r--r-- root/root 1460 2019-12-07 20:28 ./usr/share/man/man1/velvetg.1.gz -rw-r--r-- root/root 1479 2019-12-07 20:28 ./usr/share/man/man1/velvetg_de.1.gz -rw-r--r-- root/root 1422 2019-12-07 20:28 ./usr/share/man/man1/velveth.1.gz -rw-r--r-- root/root 1453 2019-12-07 20:28 ./usr/share/man/man1/velveth_de.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [566 B] Get:5 copy:/<>/apt_archive ./ Packages [650 B] Fetched 2179 B in 0s (50.8 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-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 libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 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-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils readline-common unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg liblist-someutils-xs-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-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 libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 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-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils readline-common sbuild-build-depends-lintian-dummy:amd64 unzip 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 7572 kB of archives. After this operation, 22.5 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://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-1 [49.3 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.27-3 [540 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.36.0-2 [768 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-3 [885 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40 [69.4 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b3 [11.2 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b2 [15.8 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-1+b3 [25.5 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.31-1 [24.2 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:19 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.62-1+b3 [44.2 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.25-1 [19.5 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:23 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-3+b7 [36.9 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b1 [15.3 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.27-1 [17.1 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b1 [25.3 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-1.1 [8552 B] Get:32 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.27-1 [126 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2 [36.8 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.01-2 [34.3 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libnet-netmask-perl all 2.0001-1 [32.2 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-1+b5 [103 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libdata-validate-uri-perl all 0.07-1 [10.7 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-1+b2 [25.8 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.04-1+b3 [26.7 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-2 [7448 B] Get:54 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-2 [8992 B] Get:55 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:61 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-3 [60.5 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b1 [170 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b3 [11.9 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b1 [13.5 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.120-1 [54.7 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b7 [17.0 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.008-1+b1 [11.8 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1 [46.1 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.018+ds-1+b1 [95.3 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.018+ds-1+b1 [98.3 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.21-1 [49.8 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.26-1 [28.4 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-1+b2 [27.3 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b8 [8680 B] Get:89 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1 [13.1 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-1 [195 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b3 [75.1 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b2 [19.8 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.10-1 [91.0 kB] Get:96 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get:97 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.83+ds-1 [34.2 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.22-5 [84.8 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:101 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB] Get:102 http://mirror.einval.org/debian sid/main arm64 lintian all 2.114.0 [1382 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7572 kB in 0s (41.0 MB/s) Selecting previously unselected package readline-common. (Reading database ... 26637 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.1-2_all.deb ... Unpacking readline-common (8.1-2) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../001-libreadline8_8.1-2_arm64.deb ... Unpacking libreadline8:arm64 (8.1-2) ... Selecting previously unselected package diffstat. Preparing to unpack .../002-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../003-libassuan0_2.5.5-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../004-gpgconf_2.2.27-3_arm64.deb ... Unpacking gpgconf (2.2.27-3) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../005-libsqlite3-0_3.36.0-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.36.0-2) ... Selecting previously unselected package gpg. Preparing to unpack .../006-gpg_2.2.27-3_arm64.deb ... Unpacking gpg (2.2.27-3) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../007-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../008-libapt-pkg-perl_0.1.40_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../009-libb-hooks-op-check-perl_0.22-1+b3_arm64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b3) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../010-libdynaloader-functions-perl_0.003-1.1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1.1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../011-libdevel-callchecker-perl_0.008-1+b2_arm64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b2) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../012-libparams-classify-perl_0.015-1+b3_arm64.deb ... Unpacking libparams-classify-perl (0.015-1+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../013-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../014-libtry-tiny-perl_0.31-1_all.deb ... Unpacking libtry-tiny-perl (0.31-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../015-libmodule-implementation-perl_0.09-1.1_all.deb ... Unpacking libmodule-implementation-perl (0.09-1.1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../016-libsub-exporter-progressive-perl_0.001013-1_all.deb ... 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Setting up libtext-glob-perl (0.11-2) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up liblist-compare-perl (0.55-1) ... Setting up libclone-perl (0.45-1+b1) ... Setting up libyaml-0-2:arm64 (0.2.2-1) ... Setting up libsub-identify-perl (0.14-1+b3) ... Setting up libcpanel-json-xs-perl:arm64 (4.27-1) ... Setting up libdevel-size-perl (0.83-1+b2) ... Setting up unzip (6.0-26) ... Setting up libsqlite3-0:arm64 (3.36.0-2) ... Setting up libyaml-libyaml-perl (0.83+ds-1) ... Setting up libio-interactive-perl (1.023-1) ... Setting up libtry-tiny-perl (0.31-1) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up libtime-moment-perl (0.44-1+b3) ... Setting up libassuan0:arm64 (2.5.5-1) ... Setting up libconfig-tiny-perl (2.27-1) ... Setting up libsereal-encoder-perl (4.018+ds-1+b1) ... Setting up liblist-utilsby-perl (0.11-1) ... Setting up libnet-netmask-perl (2.0001-1) ... Setting up libsub-install-perl (0.928-1.1) ... Setting up libnumber-compare-perl (0.03-2) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004003-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-1+b5) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.21-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libnet-domain-tld-perl (1.75-1.1) ... Setting up libperlio-utf8-strict-perl (0.008-1+b1) ... Setting up libio-prompt-tiny-perl (0.003-1) ... Setting up lzip (1.22-5) ... update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-1+b3) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up liblist-moreutils-xs-perl (0.430-2) ... Setting up libparams-util-perl (1.102-1+b1) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:arm64 (3.5.9-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl (0.26-1+b1) ... Setting up libsyntax-keyword-try-perl (0.26-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:arm64 (0.634-1) ... Setting up libpath-tiny-perl (0.120-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libaliased-perl (0.34-1.1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b7) ... Setting up libsort-versions-perl (1.62-1) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libterm-readkey-perl (2.38-1+b2) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libtext-levenshteinxs-perl (0.03-4+b8) ... Setting up libperlio-gzip-perl (0.19-1+b7) ... Setting up readline-common (8.1-2) ... Setting up libhtml-html5-entities-perl (0.004-1.1) ... Setting up libsereal-decoder-perl (4.018+ds-1+b1) ... Setting up libmarkdown2:arm64 (2.2.7-2) ... Setting up liburi-perl (5.10-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.04-1+b3) ... Setting up libfile-basedir-perl (0.09-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libreadline8:arm64 (8.1-2) ... Setting up libtext-markdown-discount-perl:arm64 (0.13-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libdata-validate-uri-perl (0.07-1) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up gpgconf (2.2.27-3) ... Setting up gpg (2.2.27-3) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libiterator-perl (0.03+ds1-1.1) ... Setting up libiterator-util-perl (0.02+ds1-1.1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libconst-fast-perl (0.014-1.1) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up libmoox-aliases-perl (0.001006-1.1) ... Setting up libb-hooks-endofscope-perl (0.25-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.114.0) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for man-db (2.9.4-4) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.33-1) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 80712 Build-Time: 275 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 106 Job: velvet_1.2.10+dfsg1-7 Lintian: pass Machine Architecture: arm64 Package: velvet Package-Time: 412 Source-Version: 1.2.10+dfsg1-7 Space: 80712 Status: successful Version: 1.2.10+dfsg1-7 -------------------------------------------------------------------------------- Finished at 2022-01-01T19:10:40Z Build needed 00:06:52, 80712k disk space