W: cgroups are not available on the host, not using them.
I: pbuilder: network access will be disabled during build
I: Current time: Sat May  6 18:56:21 -12 2023
I: pbuilder-time-stamp: 1683442581
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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+dfsg1-8.dsc]
I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz]
I: copying [./velvet_1.2.10+dfsg1-8.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Nov 29 07:27:31 2022 -12
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-8.dsc: no acceptable signature found
dpkg-source: info: extracting velvet in 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+dfsg1-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying include_debians_zlib.patch
dpkg-source: info: applying shuffleSequences_fasta.patch
dpkg-source: info: applying fix-perl-path.patch
dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying 2to3.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/24922/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
  DISTRIBUTION='bookworm'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='24922'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eeNxlvaV/pbuilderrc_5T6t --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eeNxlvaV/b1 --logfile b1/build.log velvet_1.2.10+dfsg1-8.dsc'
  SUDO_GID='112'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/sbin/chroot'
  http_proxy='http://78.137.99.97:3128'
I: uname -a
  Linux ionos2-i386 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux
I: ls -l /bin
  total 6036
  -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash
  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bunzip2
  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bzcat
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzcmp -> bzdiff
  -rwxr-xr-x 1 root root    2225 Sep 18  2022 bzdiff
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzegrep -> bzgrep
  -rwxr-xr-x 1 root root    4893 Nov 27  2021 bzexe
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzfgrep -> bzgrep
  -rwxr-xr-x 1 root root    3775 Sep 18  2022 bzgrep
  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bzip2
  -rwxr-xr-x 1 root root   17892 Sep 18  2022 bzip2recover
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzless -> bzmore
  -rwxr-xr-x 1 root root    1297 Sep 18  2022 bzmore
  -rwxr-xr-x 1 root root   42920 Sep 20  2022 cat
  -rwxr-xr-x 1 root root   79816 Sep 20  2022 chgrp
  -rwxr-xr-x 1 root root   67496 Sep 20  2022 chmod
  -rwxr-xr-x 1 root root   79816 Sep 20  2022 chown
  -rwxr-xr-x 1 root root  162024 Sep 20  2022 cp
  -rwxr-xr-x 1 root root  136916 Jan  5 01:20 dash
  -rwxr-xr-x 1 root root  137160 Sep 20  2022 date
  -rwxr-xr-x 1 root root  100364 Sep 20  2022 dd
  -rwxr-xr-x 1 root root  108940 Sep 20  2022 df
  -rwxr-xr-x 1 root root  162152 Sep 20  2022 dir
  -rwxr-xr-x 1 root root   87760 Mar 22 22:20 dmesg
  lrwxrwxrwx 1 root root       8 Dec 19 01:33 dnsdomainname -> hostname
  lrwxrwxrwx 1 root root       8 Dec 19 01:33 domainname -> hostname
  -rwxr-xr-x 1 root root   38760 Sep 20  2022 echo
  -rwxr-xr-x 1 root root      41 Jan 24 02:43 egrep
  -rwxr-xr-x 1 root root   34664 Sep 20  2022 false
  -rwxr-xr-x 1 root root      41 Jan 24 02:43 fgrep
  -rwxr-xr-x 1 root root   84272 Mar 22 22:20 findmnt
  -rwsr-xr-x 1 root root   30240 Mar 22 20:38 fusermount
  -rwxr-xr-x 1 root root  218680 Jan 24 02:43 grep
  -rwxr-xr-x 2 root root    2346 Apr  9  2022 gunzip
  -rwxr-xr-x 1 root root    6447 Apr  9  2022 gzexe
  -rwxr-xr-x 1 root root  100952 Apr  9  2022 gzip
  -rwxr-xr-x 1 root root   21916 Dec 19 01:33 hostname
  -rwxr-xr-x 1 root root   75756 Sep 20  2022 ln
  -rwxr-xr-x 1 root root   55600 Mar 22 23:43 login
  -rwxr-xr-x 1 root root  162152 Sep 20  2022 ls
  -rwxr-xr-x 1 root root  214568 Mar 22 22:20 lsblk
  -rwxr-xr-x 1 root root   96328 Sep 20  2022 mkdir
  -rwxr-xr-x 1 root root   84008 Sep 20  2022 mknod
  -rwxr-xr-x 1 root root   38792 Sep 20  2022 mktemp
  -rwxr-xr-x 1 root root   63016 Mar 22 22:20 more
  -rwsr-xr-x 1 root root   58912 Mar 22 22:20 mount
  -rwxr-xr-x 1 root root   13856 Mar 22 22:20 mountpoint
  -rwxr-xr-x 1 root root  157932 Sep 20  2022 mv
  lrwxrwxrwx 1 root root       8 Dec 19 01:33 nisdomainname -> hostname
  lrwxrwxrwx 1 root root      14 Apr  2 18:25 pidof -> /sbin/killall5
  -rwxr-xr-x 1 root root   38792 Sep 20  2022 pwd
  lrwxrwxrwx 1 root root       4 Apr 23 09:24 rbash -> bash
  -rwxr-xr-x 1 root root   51080 Sep 20  2022 readlink
  -rwxr-xr-x 1 root root   75720 Sep 20  2022 rm
  -rwxr-xr-x 1 root root   51080 Sep 20  2022 rmdir
  -rwxr-xr-x 1 root root   22308 Nov  2  2022 run-parts
  -rwxr-xr-x 1 root root  133224 Jan  5 07:55 sed
  lrwxrwxrwx 1 root root       4 Jan  5 01:20 sh -> dash
  -rwxr-xr-x 1 root root   38760 Sep 20  2022 sleep
  -rwxr-xr-x 1 root root   87976 Sep 20  2022 stty
  -rwsr-xr-x 1 root root   83492 Mar 22 22:20 su
  -rwxr-xr-x 1 root root   38792 Sep 20  2022 sync
  -rwxr-xr-x 1 root root  598456 Apr  6 02:25 tar
  -rwxr-xr-x 1 root root   13860 Nov  2  2022 tempfile
  -rwxr-xr-x 1 root root  120776 Sep 20  2022 touch
  -rwxr-xr-x 1 root root   34664 Sep 20  2022 true
  -rwxr-xr-x 1 root root   17892 Mar 22 20:38 ulockmgr_server
  -rwsr-xr-x 1 root root   30236 Mar 22 22:20 umount
  -rwxr-xr-x 1 root root   38760 Sep 20  2022 uname
  -rwxr-xr-x 2 root root    2346 Apr  9  2022 uncompress
  -rwxr-xr-x 1 root root  162152 Sep 20  2022 vdir
  -rwxr-xr-x 1 root root   71216 Mar 22 22:20 wdctl
  lrwxrwxrwx 1 root root       8 Dec 19 01:33 ypdomainname -> hostname
  -rwxr-xr-x 1 root root    1984 Apr  9  2022 zcat
  -rwxr-xr-x 1 root root    1678 Apr  9  2022 zcmp
  -rwxr-xr-x 1 root root    6460 Apr  9  2022 zdiff
  -rwxr-xr-x 1 root root      29 Apr  9  2022 zegrep
  -rwxr-xr-x 1 root root      29 Apr  9  2022 zfgrep
  -rwxr-xr-x 1 root root    2081 Apr  9  2022 zforce
  -rwxr-xr-x 1 root root    8103 Apr  9  2022 zgrep
  -rwxr-xr-x 1 root root    2206 Apr  9  2022 zless
  -rwxr-xr-x 1 root root    1842 Apr  9  2022 zmore
  -rwxr-xr-x 1 root root    4577 Apr  9  2022 znew
I: user script /srv/workspace/pbuilder/24922/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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-compat (= 13), 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 ... 19604 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-compat (= 13); however:
  Package debhelper-compat 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} bsdextrautils{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} isa-support{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu72{a} libkpathsea6{a} libmagic-mgc{a} libmagic1{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libptexenc1{a} libsm6{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtexluajit2{a} libtool{a} libuchardet0{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} libzzip-0-13{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} sse2-support{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 dvisvgm libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data 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, 81 newly installed, 0 to remove and 0 not upgraded.
Need to get 78.4 MB of archives. After unpacking 250 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 isa-support i386 15 [9692 B]
Get: 2 http://deb.debian.org/debian bookworm/main i386 sse2-support i386 15 [3320 B]
Get: 3 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 24 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 fonts-lmodern all 2.005-1 [4540 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libkpathsea6 i386 2022.20220321.62855-5 [155 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libptexenc1 i386 2022.20220321.62855-5 [44.6 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libsynctex2 i386 2022.20220321.62855-5 [62.2 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libteckit0 i386 2.5.11+ds1-1+b1 [282 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libtexlua53-5 i386 2022.20220321.62855-5 [126 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libtexluajit2 i386 2022.20220321.62855-5 [262 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libxmu6 i386 2:1.1.3-3 [62.5 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 libxpm4 i386 1:3.5.12-1.1 [50.0 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 libxaw7 i386 2:1.0.14-1 [209 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 libxi6 i386 2:1.8-1+b1 [86.2 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 libzzip-0-13 i386 0.13.72+dfsg.1-1.1 [60.1 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 t1utils i386 1.41-4 [62.3 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 tex-common all 6.18 [32.5 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 texlive-binaries i386 2022.20220321.62855-5 [10.6 MB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 texlive-base all 2022.20230122-3 [21.9 MB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 texlive-latex-base all 2022.20230122-3 [1182 kB]
Get: 80 http://deb.debian.org/debian bookworm/main i386 texlive-latex-recommended all 2022.20230122-3 [8880 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
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 -> Finished parsing the build-deps
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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../velvet_1.2.10+dfsg1-8_source.changes
dpkg-buildpackage: info: source package velvet
dpkg-buildpackage: info: source version 1.2.10+dfsg1-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean --no-parallel
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/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 binary
dh binary --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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 ../..
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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so
lexa2.fa solexa3.fa -long[] 

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[]\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec
ted_reads[] 

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[]\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq 
-fasta -[] 

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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_
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[]\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

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 []\OT1/cmtt/m/n/10 NODE    $NODE_ID    $COV_SHORT1   $O_COV_SHORT1  $COV_SHORT
2  $O_COV_SHORT2[] 

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[]\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) 
[19]
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[]\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv
e.co.uk)
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s_file yes[] 

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g data/test_long.fa[] 

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\OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O
MP[]NUM[]THREADS

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\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 +

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[][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/
using[]openmp.htm[][] 
[5] [6]
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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so
lexa2.fa solexa3.fa -long[] 

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[]\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec
ted_reads[] 

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[]\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq 
-fasta -[] 

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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_
specific[] 
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[]$[]$\OT1/cmr/m/n/10 . If set
[12]
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[13]
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arameters...)[] 

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[]\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads
.fa output.fa[] 
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[]\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]
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[]\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) 
[20]
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[]\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv
e.co.uk)
[21] [22] (./Manual.aux)

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(see the transcript file for additional information) </build/velvet-1.2.10+dfsg
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This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
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entering extended mode
(./Columbus_manual.tex
LaTeX2e <2022-11-01> patch level 1
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Document Class: article 2022/07/02 v1.4n Standard LaTeX document class
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[]\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped
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(see the transcript file for additional information) </build/velvet-1.2.10+dfsg
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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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/kmer.c: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:1060:49: warning: variable 'refElem' set but not used [-Wunused-but-set-variable]
 1060 |                                         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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
In file included from src/passageMarker.c:29:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/passageMarker.c: In function 'readPassageMarker':
src/passageMarker.c:291:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict]
  291 |                 sprintf(s, "%s %ld -> %ld", s,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  292 |                         (long) getNodeID(getNode(getPreviousInSequence(marker))),
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  293 |                         (long) getNodeID(getNode(marker)));
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/passageMarker.c:288:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict]
  288 |                 sprintf(s, "%s START -> %ld", s,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  289 |                         (long) getNodeID(getNode(marker)));
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/passageMarker.c:298:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict]
  298 |                 sprintf(s, "%s -> %ld ", s,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~
  299 |                         (long) getNodeID(getNode(getNextInSequence(marker))));
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/passageMarker.c:296:17: warning: 'sprintf' argument 3 overlaps destination object 's' [-Wrestrict]
  296 |                 sprintf(s, "%s -> FINISH", s);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:1961:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat=]
 1961 |                 sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
      |                                                              ~~^                  ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                |                                     |
      |                                                                long int                              long long int
      |                                                              %lld
In file included from src/graphStats.c:28:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 *' [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
In function 'addMapping',
    inlined from 'readCigar' at src/readSet.c:796:6:
src/readSet.c:750:25: warning: 'snprintf' argument 4 overlaps destination object 'buffer' [-Wrestrict]
  750 |                         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 'readCigar':
src/readSet.c:783:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
  783 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {
      |                                                                                                                      ~~~~~~~^~~~~~
In function 'addMapping',
    inlined from 'readCigar' at src/readSet.c:796:6:
src/readSet.c:748:25: warning: 'snprintf' argument 4 overlaps destination object 'buffer' [-Wrestrict]
  748 |                         snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) orientation * refCoord->referenceID, (long long) (pos - refCoord->start));
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/readSet.c: In function 'readCigar':
src/readSet.c:783:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
  783 | static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {
      |                                                                                                                      ~~~~~~~^~~~~~
src/readSet.c: In function 'importReadSet':
src/readSet.c:1613:25: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
 1613 |                         strncpy(sequence + bpCount, line, lineLength);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/readSet.c:1612:38: note: length computed here
 1612 |                         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:304:90: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                          ^
src/binarySequences.c:304:132: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                                                                    ^
src/binarySequences.c:304:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                     ~~^                                  ~~~~~~~~~~~~~~
      |                                                       |                                  |
      |                                                       long unsigned int                  long long unsigned int
      |                                                     %llx
src/binarySequences.c:304:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                 ~~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                   |                                      |
      |                                                                   long int                               long long unsigned int
      |                                                                 %lld
src/binarySequences.c:304:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat=]
  304 |                         velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
      |                                                                                  ~~^                                               ~~~~~~~~~~~~~~~~~~~
      |                                                                                    |                                               |
      |                                                                                    long unsigned int                               long long unsigned int
      |                                                                                  %llx
src/binarySequences.c:314:33: warning: variable 'refElem' set but not used [-Wunused-but-set-variable]
  314 |                         RefInfo refElem;
      |                                 ^~~~~~~
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:389:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  389 |         velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
      |                                  ~~^               ~~~~~~
      |                                    |               |
      |                                    long int        uint64_t {aka long long unsigned int}
      |                                  %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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 
src/preGraph.c: In function 'addPreArcToPreNode_pg':
src/preGraph.c:165:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  165 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  167 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c: In function 'removePreArcFromList_pg':
src/preGraph.c:285:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  285 |                 preArcPtr = &(preNode->preArcRight);
      |                             ^~~~~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:29: warning: taking address of packed member of 'struct preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  287 |                 preArcPtr = &(preNode->preArcLeft);
      |                             ^~~~~~~~~~~~~~~~~~~~~~
In file included from src/run.h:34,
                 from src/preGraph.c:35:
src/graph.h: At top level:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:414:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  414 |         if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file))
      |         ^~
src/preGraphConstruction.c:416:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  416 |                 seqReadInfo->m_pFile = file;
      |                 ^~~~~~~~~~~
src/preGraphConstruction.c:525:72: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                      ~~^                           ~~~~~~~~~~~~~~~~~~~~
      |                                                                        |                           |
      |                                                                        long int                    long long unsigned int
      |                                                                      %lld
src/preGraphConstruction.c:525:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  525 |                                                 velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
      |                                                                                            ~~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                              |                           |
      |                                                                                              long int                    long long unsigned int
      |                                                                                            %lld
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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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: In function 'pushNucleotide':
src/kmer.c:419:15: warning: taking address of packed member of 'struct kmer_st' may result in an unaligned pointer value [-Waddress-of-packed-member]
  419 |         ptr = kmer->longlongs;
      |               ^~~~
src/kmer.c: At top level:
src/kmer.c:31:22: warning: 'charLeftFilter' defined but not used [-Wunused-const-variable=]
   31 | static const uint8_t charLeftFilter = (uint8_t) 3 << 6;
      |                      ^~~~~~~~~~~~~~
src/kmer.c:30:23: warning: 'intLeftFilter' defined but not used [-Wunused-const-variable=]
   30 | static const uint16_t intLeftFilter = (uint16_t) 3 << 14;
      |                       ^~~~~~~~~~~~~
src/kmer.c:29:23: warning: 'longLeftFilter' defined but not used [-Wunused-const-variable=]
   29 | static const uint32_t longLeftFilter = (uint32_t) 3 << 30;
      |                       ^~~~~~~~~~~~~~
src/kmer.c:28:23: warning: 'longLongLeftFilter' defined but not used [-Wunused-const-variable=]
   28 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
  173 | 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:49:13: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
   49 |         int rc, status;
      |             ^~
src/autoOpen.c: At top level:
src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier]
   56 | 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
[Sat May 06 19:01:44 2023] Running Velvet Test Suite
[Sat May 06 19:01:44 2023] Found ../velveth, ok
[Sat May 06 19:01:44 2023] Found ../velvetg, ok
[Sat May 06 19:01:44 2023] Found Sequences.31, ok
[Sat May 06 19:01:44 2023] Found Roadmaps.31, ok
[Sat May 06 19:01:44 2023] Found read1.fq.gz, ok
[Sat May 06 19:01:44 2023] Found read2.fq.gz, ok
[Sat May 06 19:01:44 2023] Found reads.fq.gz, ok
[Sat May 06 19:01:44 2023] Found read1.fa.gz, ok
[Sat May 06 19:01:44 2023] Found read2.fa.gz, ok
[Sat May 06 19:01:44 2023] Found reads.fa.gz, ok
[Sat May 06 19:01:44 2023] making test folder: velvet.test.z8Gq8u
[Sat May 06 19:01:44 2023] running test 1 of 5: fasta_eq_fastq_ascii.t
[Sat May 06 19:01:46 2023] ok
[Sat May 06 19:01:46 2023] ok
[Sat May 06 19:01:46 2023] ok
[Sat May 06 19:01:46 2023] ok
[Sat May 06 19:01:46 2023] passed test 1
[Sat May 06 19:01:46 2023] running test 2 of 5: fasta_eq_fastq_binary.t
[Sat May 06 19:01:49 2023] ok
[Sat May 06 19:01:49 2023] ok
[Sat May 06 19:01:49 2023] passed test 2
[Sat May 06 19:01:49 2023] running test 3 of 5: fmt_auto_mode.t
[Sat May 06 19:01:51 2023] ok
[Sat May 06 19:01:51 2023] ok
[Sat May 06 19:01:51 2023] passed test 3
[Sat May 06 19:01:51 2023] running test 4 of 5: interleaved_eq_separate.t
[Sat May 06 19:01:57 2023] ok
[Sat May 06 19:01:57 2023] ok
[Sat May 06 19:01:57 2023] passed test 4
[Sat May 06 19:01:57 2023] running test 5 of 5: mismatched_separates.t
[Sat May 06 19:01:57 2023] ok
[Sat May 06 19:01:57 2023] ok
[Sat May 06 19:01:57 2023] passed test 5
[Sat May 06 19:01:57 2023] removing test folder: velvet.test.z8Gq8u
[Sat May 06 19:01:57 2023] passed all 5 tests
[Sat May 06 19:01:57 2023] hooray!
make[1]: Leaving directory '/build/velvet-1.2.10+dfsg1'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--no-parallel
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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
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make[1]: Entering directory '/build/velvet-1.2.10+dfsg1'
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dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-8_i386.deb'.
dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-8_i386.deb'.
dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-8_i386.deb'.
dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-8_i386.deb'.
dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-8_all.deb'.
dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-8_all.deb'.
 dpkg-genbuildinfo --build=binary -O../velvet_1.2.10+dfsg1-8_i386.buildinfo
 dpkg-genchanges --build=binary -O../velvet_1.2.10+dfsg1-8_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)
dpkg-genchanges: info: not including original source code in upload
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/24922 and its subdirectories
I: Current time: Sat May  6 19:02:53 -12 2023
I: pbuilder-time-stamp: 1683442973