Sat May 23 05:05:26 UTC 2020 I: starting to build velvet/buster/i386 on jenkins on '2020-05-23 05:05' Sat May 23 05:05:26 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/6088/console.log Sat May 23 05:05:26 UTC 2020 I: Downloading source for buster/velvet=1.2.10+dfsg1-5 --2020-05-23 05:05:26-- http://deb.debian.org/debian/pool/main/v/velvet/velvet_1.2.10+dfsg1-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2268 (2.2K) Saving to: ‘velvet_1.2.10+dfsg1-5.dsc’ 0K .. 100% 89.1M=0s 2020-05-23 05:05:26 (89.1 MB/s) - ‘velvet_1.2.10+dfsg1-5.dsc’ saved [2268/2268] Sat May 23 05:05:26 UTC 2020 I: velvet_1.2.10+dfsg1-5.dsc -----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+dfsg1-5 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/velvet Vcs-Git: https://salsa.debian.org/med-team/velvet.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), 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 102568fa9694e1ad466453a2e5c98c970dda89e7 14248 velvet_1.2.10+dfsg1-5.debian.tar.xz Checksums-Sha256: 368d760ad56ffa010a2ae72b25d46680ecb7ad8cc573cf6c389848c87b32ee26 13630488 velvet_1.2.10+dfsg1.orig.tar.xz e89d1ab45b9a608a37343c7710e05ec3c3d593d396aecc1c5ece2b2d298b8dd3 14248 velvet_1.2.10+dfsg1-5.debian.tar.xz Files: 7a58a6d75cdc8b89d1c605033050bbcf 13630488 velvet_1.2.10+dfsg1.orig.tar.xz 4a31d0b7b3bda01bd4479420b8d3b185 14248 velvet_1.2.10+dfsg1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAls92yARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFpZw/9EGeTnUW1thPGsiE3dHUmIM6/VqMCuWNE bvXTEED/iSR7NJov5B8xm2H/5fd8ykRB8D3SMEgEuIiWa9ZxnZxQE4b8tLcBz/oD d8CfKKF/YFUP3G712wPyA3B3Ug51MbmUpeNj57eKtg87ePkUnSW2rJfuFUtHBw4K pyO+i5DZjEBBZHZbTomtv1sOVTlTt7Q2UL7Fg+cyFUBQC2a74gn1+Tkjoi/NYO2b zFBlxPXyMKfcPgeNJVlHg3rx9OKBux8u7sZjdKhlUVp2trLTJyzaAM9qQ7gpC7L4 /hhdJNjWUf7/eGEXlTH7Z5HXZXgfIXITrOvTy1b/35GdKsZ+0KT0qYozCzCQ6Oz3 VJRXpx9eH0yWgp/BHwg0C/8zbumu2se0FCmk2OfKODSqKzdBDhGVjq/I0z8lNm6d Ix1++F7ILlI4uEVwBSIQnuDJKB/o6RSRvAGSubcqv1y7SBhus/6y6NOUhB5crFHX TYpy4aYTa4twotZrK4OUo6/UW9XSQAMva2iycguC+69GD+ZA9HxCymsv/sb8ifi6 rAxNW+delQ6uUIFfdKRhEUR32NFvNeYXLULgWAW+YMztT4DIy3l+dE6C4yoKmXP1 OIIMOp6SXr/EBodc1JOEsXTW+egnzgE1M8vX5NMIGgqe1D9DG1wc5qt2IGd8CWVh oSCah0u7Cog= =FASv -----END PGP SIGNATURE----- Sat May 23 05:05:26 UTC 2020 I: Checking whether the package is not for us Sat May 23 05:05:26 UTC 2020 I: Starting 1st build on remote node profitbricks-build6-i386.debian.net. Sat May 23 05:05:26 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build6-i386.debian.net. Sat May 23 05:08:02 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 24 23:28:24 -12 2021 I: pbuilder-time-stamp: 1624620504 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [velvet_1.2.10+dfsg1-5.dsc] I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz] I: copying [./velvet_1.2.10+dfsg1-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 4 20:47:28 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./velvet_1.2.10+dfsg1-5.dsc dpkg-source: info: extracting velvet in velvet-1.2.10+dfsg1 dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-5.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 I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), zlib1g-dev, texlive-latex-base, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcroco3{a} libcups2{a} libcupsimage2{a} libdbus-1-3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libgraphite2-3{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libice6{a} libicu63{a} libidn11{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libopenjp2-7{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpotrace0{a} libptexenc1{a} libsigsegv2{a} libsm6{a} libssl1.1{a} libsynctex2{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtexluajit2{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwoff1{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} po-debconf{a} poppler-data{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} ucf{a} x11-common{a} xdg-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus fonts-droid-fallback krb5-locales libarchive-cpio-perl libcupsfilters1 libfile-mimeinfo-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 110 newly installed, 0 to remove and 0 not upgraded. Need to get 94.9 MB of archives. After unpacking 306 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 poppler-data all 0.4.9-2 [1473 kB] Get: 8 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main i386 ucf all 3.0038+nmu1 [69.0 kB] Get: 10 http://deb.debian.org/debian buster/main i386 tex-common all 6.11 [53.1 kB] Get: 11 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 13 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 14 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 16 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 18 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 19 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 20 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 24 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 25 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 27 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 30 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 31 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 32 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 33 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 34 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 35 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 36 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 37 http://deb.debian.org/debian buster/main i386 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 38 http://deb.debian.org/debian buster/main i386 fontconfig-config all 2.13.1-2 [280 kB] Get: 39 http://deb.debian.org/debian buster/main i386 fonts-lmodern all 2.004.5-6 [4539 kB] Get: 40 http://deb.debian.org/debian buster/main i386 libavahi-common-data i386 0.7-4+b1 [122 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libavahi-common3 i386 0.7-4+b1 [56.2 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libdbus-1-3 i386 1.12.16-1 [226 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libavahi-client3 i386 0.7-4+b1 [60.1 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libbrotli1 i386 1.0.7-2 [267 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libpng16-16 i386 1.6.36-6 [301 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libfreetype6 i386 2.9.1-3+deb10u1 [395 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libfontconfig1 i386 2.13.1-2 [357 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libpixman-1-0 i386 0.36.0-1 [541 kB] Get: 50 http://deb.debian.org/debian buster/main i386 libxau6 i386 1:1.0.8-1+b2 [20.3 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libxcb1 i386 1.13.1-2 [141 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libx11-data all 2:1.6.7-1 [298 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libx11-6 i386 2:1.6.7-1 [778 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libxcb-render0 i386 1.13.1-2 [110 kB] Get: 56 http://deb.debian.org/debian buster/main i386 libxcb-shm0 i386 1.13.1-2 [99.4 kB] Get: 57 http://deb.debian.org/debian buster/main i386 libxext6 i386 2:1.3.3-1+b2 [55.2 kB] Get: 58 http://deb.debian.org/debian buster/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 59 http://deb.debian.org/debian buster/main i386 libcairo2 i386 1.16.0-4 [744 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libkeyutils1 i386 1.6-6 [15.4 kB] Get: 61 http://deb.debian.org/debian buster/main i386 libkrb5support0 i386 1.17-3 [68.6 kB] Get: 62 http://deb.debian.org/debian buster/main i386 libk5crypto3 i386 1.17-3 [126 kB] Get: 63 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 64 http://deb.debian.org/debian buster/main i386 libkrb5-3 i386 1.17-3 [396 kB] Get: 65 http://deb.debian.org/debian buster/main i386 libgssapi-krb5-2 i386 1.17-3 [168 kB] Get: 66 http://deb.debian.org/debian buster/main i386 libcups2 i386 2.2.10-6+deb10u3 [338 kB] Get: 67 http://deb.debian.org/debian buster/main i386 libcupsimage2 i386 2.2.10-6+deb10u3 [133 kB] Get: 68 http://deb.debian.org/debian buster/main i386 libgraphite2-3 i386 1.3.13-7 [84.0 kB] Get: 69 http://deb.debian.org/debian buster/main i386 libgs9-common all 9.27~dfsg-2+deb10u3 [5136 kB] Get: 70 http://deb.debian.org/debian buster/main i386 libidn11 i386 1.33-2.2 [116 kB] Get: 71 http://deb.debian.org/debian buster/main i386 libijs-0.35 i386 0.35-14 [18.9 kB] Get: 72 http://deb.debian.org/debian buster/main i386 libjbig2dec0 i386 0.16-1 [64.6 kB] Get: 73 http://deb.debian.org/debian buster/main i386 libjpeg62-turbo i386 1:1.5.2-2+b1 [142 kB] Get: 74 http://deb.debian.org/debian buster/main i386 liblcms2-2 i386 2.9-3 [156 kB] Get: 75 http://deb.debian.org/debian buster/main i386 libopenjp2-7 i386 2.3.0-2+deb10u1 [164 kB] Get: 76 http://deb.debian.org/debian buster/main i386 libpaper1 i386 1.1.28 [21.4 kB] Get: 77 http://deb.debian.org/debian buster/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 78 http://deb.debian.org/debian buster/main i386 libwebp6 i386 0.6.1-2 [275 kB] Get: 79 http://deb.debian.org/debian buster/main i386 libtiff5 i386 4.1.0+git191117-2~deb10u1 [284 kB] Get: 80 http://deb.debian.org/debian buster/main i386 libgs9 i386 9.27~dfsg-2+deb10u3 [2300 kB] Get: 81 http://deb.debian.org/debian buster/main i386 libharfbuzz0b i386 2.3.1-1 [1209 kB] Get: 82 http://deb.debian.org/debian buster/main i386 libharfbuzz-icu0 i386 2.3.1-1 [834 kB] Get: 83 http://deb.debian.org/debian buster/main i386 lsb-base all 10.2019051400 [28.4 kB] Get: 84 http://deb.debian.org/debian buster/main i386 x11-common all 1:7.7+19 [251 kB] Get: 85 http://deb.debian.org/debian buster/main i386 libice6 i386 2:1.0.9-2 [61.1 kB] Get: 86 http://deb.debian.org/debian buster/main i386 libkpathsea6 i386 2018.20181218.49446-1 [171 kB] Get: 87 http://deb.debian.org/debian buster/main i386 libpaper-utils i386 1.1.28 [18.3 kB] Get: 88 http://deb.debian.org/debian buster/main i386 libpotrace0 i386 1.15-1 [25.6 kB] Get: 89 http://deb.debian.org/debian buster/main i386 libptexenc1 i386 2018.20181218.49446-1 [61.6 kB] Get: 90 http://deb.debian.org/debian buster/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 91 http://deb.debian.org/debian buster/main i386 libsynctex2 i386 2018.20181218.49446-1 [83.5 kB] Get: 92 http://deb.debian.org/debian buster/main i386 libteckit0 i386 2.5.8+ds2-5 [268 kB] Get: 93 http://deb.debian.org/debian buster/main i386 libtexlua52 i386 2018.20181218.49446-1 [121 kB] Get: 94 http://deb.debian.org/debian buster/main i386 libtexlua53 i386 2018.20181218.49446-1 [141 kB] Get: 95 http://deb.debian.org/debian buster/main i386 libtexluajit2 i386 2018.20181218.49446-1 [270 kB] Get: 96 http://deb.debian.org/debian buster/main i386 libwoff1 i386 1.0.2-1 [46.0 kB] Get: 97 http://deb.debian.org/debian buster/main i386 libxt6 i386 1:1.1.5-1+b3 [195 kB] Get: 98 http://deb.debian.org/debian buster/main i386 libxmu6 i386 2:1.1.2-2+b3 [62.8 kB] Get: 99 http://deb.debian.org/debian buster/main i386 libxpm4 i386 1:3.5.12-1 [50.9 kB] Get: 100 http://deb.debian.org/debian buster/main i386 libxaw7 i386 2:1.0.13-1+b2 [209 kB] Get: 101 http://deb.debian.org/debian buster/main i386 libxi6 i386 2:1.7.9-1 [85.2 kB] Get: 102 http://deb.debian.org/debian buster/main i386 libxxhash0 i386 0.6.5-2 [8788 B] Get: 103 http://deb.debian.org/debian buster/main i386 libzzip-0-13 i386 0.13.62-3.2 [57.3 kB] Get: 104 http://deb.debian.org/debian buster/main i386 t1utils i386 1.41-3 [62.2 kB] Get: 105 http://deb.debian.org/debian buster/main i386 texlive-binaries i386 2018.20181218.49446-1 [11.2 MB] Get: 106 http://deb.debian.org/debian buster/main i386 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 107 http://deb.debian.org/debian buster/main i386 texlive-base all 2018.20190227-2 [19.7 MB] Get: 108 http://deb.debian.org/debian buster/main i386 texlive-latex-base all 2018.20190227-2 [984 kB] Get: 109 http://deb.debian.org/debian buster/main i386 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get: 110 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Fetched 94.9 MB in 2s (48.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../002-libuchardet0_0.0.6-3_i386.deb ... 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This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/velvet-1.2.10+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/velvet-1.2.10+dfsg1' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory rm: cannot remove './velvet*': No such file or directory make[2]: [Makefile:45: clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory '/build/velvet-1.2.10+dfsg1' rm -rf zlib rm -rf third-party rm -rf debian.upstream rm -f *.pdf find -name '._*' -delete rm -rf contrib/MetaVelvet* rm -rf contrib/VelvetOptimiser* make[1]: Leaving directory '/build/velvet-1.2.10+dfsg1' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules build dh build --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/velvet-1.2.10+dfsg1' touch zlib #Make _long version dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 '/build/velvet-1.2.10+dfsg1' mv velveth velveth_long ; mv velvetg velvetg_long #Make _63 kmer version dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 '/build/velvet-1.2.10+dfsg1' mv velveth velveth_63 ; mv velvetg velvetg_63 #And also one with both options dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 '/build/velvet-1.2.10+dfsg1' mv velveth velveth_63_long ; mv velvetg velvetg_63_long #Make _127 kmer version dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 '/build/velvet-1.2.10+dfsg1' mv velveth velveth_127 ; mv velvetg velvetg_127 #And also one with both options dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 '/build/velvet-1.2.10+dfsg1' mv velveth velveth_127_long ; mv velvetg velvetg_127_long touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i 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/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.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))) 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/generic/oberdiek/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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) 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) Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. 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 (21 pages, 422893 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i 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/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.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))) (./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/generic/oberdiek/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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] [6] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov [15] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) 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, 430447 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) 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] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [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) ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 90158 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/build/velvet-1.2.10+dfsg1' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -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 '/build/velvet-1.2.10+dfsg1' make[1]: Leaving directory '/build/velvet-1.2.10+dfsg1' dh_auto_test -O--no-parallel make -j1 test make[1]: Entering directory '/build/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[1]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:14: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] RefInfo refElem; ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o src/passageMarker.c: In function 'readPassageMarker': src/passageMarker.c:289:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] (long) getNodeID(getNode(marker))); ^ src/passageMarker.c:293:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] (long) getNodeID(getNode(marker))); ^ src/passageMarker.c:296:3: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(s, "%s -> FINISH", s); ^~~~~~~ src/passageMarker.c:299:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] (long) getNodeID(getNode(getNextInSequence(marker)))); ^ In file included from src/passageMarker.c:29: src/passageMarker.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:50: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=] sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1); ~~^ ~~~~~~~~~~~~~~~~~~~~~~ %lld In file included from src/graphStats.c:28: src/graphStats.c: At top level: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] 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 *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'addMapping': src/readSet.c:748:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) orientation * refCoord->referenceID, (long long) (pos - refCoord->start)); ^~~~~~~~ src/readSet.c:750:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) - orientation * refCoord->referenceID, (long long) (refCoord->finish - pos - strlen(seq))); ^~~~~~~~ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:304:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ^ src/binarySequences.c:304:34: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~ %llx src/binarySequences.c:304:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ %lld src/binarySequences.c:304:63: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=] velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd); ~~^ ~~~~~~~~~~~~~~~~~~~ %llx src/binarySequences.c:314:12: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] RefInfo refElem; ^~~~~~~ src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:389:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] velvetLog("CnySeq bufIdx %ld too large\n", bufIdx); ~~^ ~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:414:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file)) ^~ src/preGraphConstruction.c:416:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' seqReadInfo->m_pFile = file; ^~~~~~~~~~~ src/preGraphConstruction.c:525:30: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~ %lld src/preGraphConstruction.c:525:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=] velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length); ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c:31:22: warning: 'charLeftFilter' defined but not used [-Wunused-const-variable=] static const uint8_t charLeftFilter = (uint8_t) 3 << 6; ^~~~~~~~~~~~~~ src/kmer.c:30:23: warning: 'intLeftFilter' defined but not used [-Wunused-const-variable=] static const uint16_t intLeftFilter = (uint16_t) 3 << 14; ^~~~~~~~~~~~~ src/kmer.c:29:23: warning: 'longLeftFilter' defined but not used [-Wunused-const-variable=] static const uint32_t longLeftFilter = (uint32_t) 3 << 30; ^~~~~~~~~~~~~~ src/kmer.c:28:23: warning: 'longLongLeftFilter' defined but not used [-Wunused-const-variable=] static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; ^~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'pcloseNoStderr': src/autoOpen.c:49:6: warning: variable 'rc' set but not used [-Wunused-but-set-variable] int rc, status; ^~ src/autoOpen.c: At top level: src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL}; ^~~~~ gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm gcc -g -O2 -ffile-prefix-map=/build/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cd tests && ./run-tests.sh [Thu Jun 24 23:30:23 2021] Running Velvet Test Suite [Thu Jun 24 23:30:23 2021] Found ../velveth, ok [Thu Jun 24 23:30:23 2021] Found ../velvetg, ok [Thu Jun 24 23:30:23 2021] Found Sequences.31, ok [Thu Jun 24 23:30:23 2021] Found Roadmaps.31, ok [Thu Jun 24 23:30:23 2021] Found read1.fq.gz, ok [Thu Jun 24 23:30:23 2021] Found read2.fq.gz, ok [Thu Jun 24 23:30:23 2021] Found reads.fq.gz, ok [Thu Jun 24 23:30:23 2021] Found read1.fa.gz, ok [Thu Jun 24 23:30:23 2021] Found read2.fa.gz, ok [Thu Jun 24 23:30:23 2021] Found reads.fa.gz, ok [Thu Jun 24 23:30:23 2021] making test folder: velvet.test.nt4klu [Thu Jun 24 23:30:23 2021] running test 1 of 5: fasta_eq_fastq_ascii.t [Thu Jun 24 23:30:24 2021] ok [Thu Jun 24 23:30:24 2021] ok [Thu Jun 24 23:30:24 2021] ok [Thu Jun 24 23:30:24 2021] ok [Thu Jun 24 23:30:24 2021] passed test 1 [Thu Jun 24 23:30:24 2021] running test 2 of 5: fasta_eq_fastq_binary.t [Thu Jun 24 23:30:25 2021] ok [Thu Jun 24 23:30:25 2021] ok [Thu Jun 24 23:30:25 2021] passed test 2 [Thu Jun 24 23:30:25 2021] running test 3 of 5: fmt_auto_mode.t [Thu Jun 24 23:30:26 2021] ok [Thu Jun 24 23:30:26 2021] ok [Thu Jun 24 23:30:26 2021] passed test 3 [Thu Jun 24 23:30:26 2021] running test 4 of 5: interleaved_eq_separate.t [Thu Jun 24 23:30:29 2021] ok [Thu Jun 24 23:30:29 2021] ok [Thu Jun 24 23:30:29 2021] passed test 4 [Thu Jun 24 23:30:29 2021] running test 5 of 5: mismatched_separates.t [Thu Jun 24 23:30:29 2021] ok [Thu Jun 24 23:30:29 2021] ok [Thu Jun 24 23:30:29 2021] passed test 5 [Thu Jun 24 23:30:29 2021] removing test folder: velvet.test.nt4klu [Thu Jun 24 23:30:29 2021] passed all 5 tests [Thu Jun 24 23:30:29 2021] hooray! make[1]: Leaving directory '/build/velvet-1.2.10+dfsg1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --no-parallel dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel debian/rules override_dh_install make[1]: Entering directory '/build/velvet-1.2.10+dfsg1' dh_install # remove extra copies of GPL find /build/velvet-1.2.10+dfsg1/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 '/build/velvet-1.2.10+dfsg1' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/velvet-1.2.10+dfsg1' dh_installexamples -i xz -6 debian/velvet-example/usr/share/doc/velvet/examples/* sed -i 's?=\.\./velvet?=/usr/bin/velvet?' debian/velvet-tests/usr/share/doc/velvet/tests/run-tests.functions make[1]: Leaving directory '/build/velvet-1.2.10+dfsg1' dh_installman -O--no-parallel dh_installinit -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/build/velvet-1.2.10+dfsg1' dh_compress -X.pdf -X.c -X.pl -X.h -X.xz make[1]: Leaving directory '/build/velvet-1.2.10+dfsg1' dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_strip -O--no-parallel dh_makeshlibs -O--no-parallel dh_shlibdeps -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-5_i386.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-5_i386.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-5_i386.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-5_i386.deb'. dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-5_all.deb'. dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../velvet_1.2.10+dfsg1-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/13528 and its subdirectories I: Current time: Thu Jun 24 23:30:58 -12 2021 I: pbuilder-time-stamp: 1624620658 Sat May 23 05:08:03 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build2-i386.debian.net. Sat May 23 05:08:03 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build2-i386.debian.net. Sat May 23 05:20:40 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. Sat May 23 05:20:40 UTC 2020 I: velvet_1.2.10+dfsg1-5_i386.changes: Format: 1.8 Date: Thu, 05 Jul 2018 10:17:41 +0200 Source: velvet Binary: velvet velvet-dbgsym velvet-example velvet-long velvet-long-dbgsym velvet-tests Architecture: i386 all Version: 1.2.10+dfsg1-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler velvet-long - Nucleic acid sequence assembler for very short reads, long versio velvet-tests - Test data for the Velvet sequence assembler Changes: velvet (1.2.10+dfsg1-5) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata: Added references to registries. . [ Andreas Tille ] * drop unneeded get-orig-source target * debhelper 11 (--no-parallel needed) * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * d/control: Drop unnecessary Testsuite field * Provide manpages for versions with MAXKMERLENGTH = 127 * Try better hardening but failed (hints are welcome) * Fix spelling * Secure URI in watch file * Remove unused lintian override Checksums-Sha1: 5ace6ee2532abfa842020454f1b90af2b3c8c8e1 904388 velvet-dbgsym_1.2.10+dfsg1-5_i386.deb 5ef0596b4b642276fe70539a4c805f5bdbc0d3a3 3335332 velvet-example_1.2.10+dfsg1-5_all.deb 2079b36d2e263e03dafdb34b0c887e612d918d41 1986536 velvet-long-dbgsym_1.2.10+dfsg1-5_i386.deb 089ba2cba91bce0b5a31fcd5b722bd449a40ecf5 254812 velvet-long_1.2.10+dfsg1-5_i386.deb e106dfbfc62909c598fcebc94f869cf39480bb3a 10752740 velvet-tests_1.2.10+dfsg1-5_all.deb 29a63ba5d362f9b371576cea33286f40f0934f47 8323 velvet_1.2.10+dfsg1-5_i386.buildinfo 6636e645c5c69df61c8551a097bc6a84dd5db7b1 703508 velvet_1.2.10+dfsg1-5_i386.deb Checksums-Sha256: 55b940077f3d99767aade3cf220120e68907892c21102acb89428ba7e30d8aca 904388 velvet-dbgsym_1.2.10+dfsg1-5_i386.deb 7cdd3533979d870aee62e37770c226a0a92680eb2f2b712af209e1ff7c0ca5b8 3335332 velvet-example_1.2.10+dfsg1-5_all.deb 5ffc62b820cc1ab20a5648f6aae2c32370fba3fe9262646b7b9e74e18a8231a9 1986536 velvet-long-dbgsym_1.2.10+dfsg1-5_i386.deb 58d9dfc3c58323c697e50b411e0e9747f6f5a32fe065afe755a5f72f9baffd38 254812 velvet-long_1.2.10+dfsg1-5_i386.deb 8825bcd3e7fad9ef45e9291e32a0094d9196adfd69b9f3bd6b664bbc797acc1b 10752740 velvet-tests_1.2.10+dfsg1-5_all.deb 00066f747f1ef841b314cb4415de912a268ee20edf3d85bd77cd3d760a4a7e51 8323 velvet_1.2.10+dfsg1-5_i386.buildinfo d981ada968758f26fb9e465561a98d12145002a6993a67bd8d85956ba5ab33b5 703508 velvet_1.2.10+dfsg1-5_i386.deb Files: 33209cf11aae748131887fa53888cd82 904388 debug optional velvet-dbgsym_1.2.10+dfsg1-5_i386.deb 2e7e7c8fade12e58579c1bce875a8b4d 3335332 science optional velvet-example_1.2.10+dfsg1-5_all.deb b18d45de9453ac388dd17d559249e198 1986536 debug optional velvet-long-dbgsym_1.2.10+dfsg1-5_i386.deb 58c6d63bfa57a8e2180efd222938cffe 254812 science optional velvet-long_1.2.10+dfsg1-5_i386.deb dc680ddc3a0637c19b93926e8c6eb277 10752740 science optional velvet-tests_1.2.10+dfsg1-5_all.deb 07695ca8a8607c4e4d7b05b34999fc47 8323 science optional velvet_1.2.10+dfsg1-5_i386.buildinfo 3d8b19d899eba814afb90fdaa92c4b60 703508 science optional velvet_1.2.10+dfsg1-5_i386.deb Sat May 23 05:20:41 UTC 2020 I: diffoscope 144 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.fXBR8UBQ4V/velvet_1.2.10+dfsg1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.fXBR8UBQ4V/velvet_1.2.10+dfsg1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.fXBR8UBQ4V/velvet_1.2.10+dfsg1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.fXBR8UBQ4V/b1/velvet_1.2.10+dfsg1-5_i386.changes /srv/reproducible-results/rbuild-debian/tmp.fXBR8UBQ4V/b2/velvet_1.2.10+dfsg1-5_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.341s) 0.341s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.125s) 0.125s 10 calls diffoscope.comparators.binary.FilesystemFile Sat May 23 05:20:43 UTC 2020 I: diffoscope 144 found no differences in the changes files, and a .buildinfo file also exists. Sat May 23 05:20:43 UTC 2020 I: velvet from buster built successfully and reproducibly on i386. Sat May 23 05:20:45 UTC 2020 I: Submitting .buildinfo files to external archives: Sat May 23 05:20:45 UTC 2020 I: Submitting 12K b1/velvet_1.2.10+dfsg1-5_i386.buildinfo.asc Sat May 23 05:20:46 UTC 2020 I: Submitting 12K b2/velvet_1.2.10+dfsg1-5_i386.buildinfo.asc Sat May 23 05:20:47 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 23 05:20:47 UTC 2020 I: Done submitting .buildinfo files. Sat May 23 05:20:47 UTC 2020 I: Removing signed velvet_1.2.10+dfsg1-5_i386.buildinfo.asc files: removed './b1/velvet_1.2.10+dfsg1-5_i386.buildinfo.asc' removed './b2/velvet_1.2.10+dfsg1-5_i386.buildinfo.asc'