I: pbuilder: network access will be disabled during build
I: Current time: Tue Mar 24 18:37:36 -12 2026
I: pbuilder-time-stamp: 1774420656
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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+dfsg1-9.dsc]
I: copying [./velvet_1.2.10+dfsg1.orig.tar.xz]
I: copying [./velvet_1.2.10+dfsg1-9.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./velvet_1.2.10+dfsg1-9.dsc: unsupported subcommand
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+dfsg1-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying include_debians_zlib.patch
dpkg-source: info: applying shuffleSequences_fasta.patch
dpkg-source: info: applying fix-perl-path.patch
dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying gcc-14.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/436/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
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=22 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='8b0ed7883aad4aa3ae4eba1175b677d7'
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='436'
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.RjnhvMTy/pbuilderrc_6T7n --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RjnhvMTy/b1 --logfile b1/build.log velvet_1.2.10+dfsg1-9.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos16-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/436/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 ... 19795 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-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu72{a} libkpathsea6{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libpaper-utils{a} libpaper2{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libsm6{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libtool{a} libuchardet0{a} libunistring5{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} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} ucf{a} x11-common{a} xdg-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl dvisvgm libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded.
Need to get 78.3 MB of archives. After unpacking 244 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-7 [66.0 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-7 [876 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 libtext-charwidth-perl i386 0.04-11+b4 [9656 B]
Get: 14 http://deb.debian.org/debian trixie/main i386 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 15 http://deb.debian.org/debian trixie/main i386 ucf all 3.0049 [42.5 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 27 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-2 [317 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 fonts-lmodern all 2.005-1 [4540 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.46-4 [292 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-2 [402 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b3 [52.5 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b4 [28.8 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.83.3-2 [1581 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.2.0-1 [504 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+24 [217 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.1.1-1 [67.8 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 libkpathsea6 i386 2024.20240313.70630+ds-5+b1 [160 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 libmpfi0 i386 1.5.4+ds-4 [38.8 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libpaper2 i386 2.2.5-0.3+b1 [17.1 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 2.2.5-0.3+b1 [16.4 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 libpotrace0 i386 1.16-2+b2 [24.5 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libptexenc1 i386 2024.20240313.70630+ds-5+b1 [50.3 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 libsynctex2 i386 2024.20240313.70630+ds-5+b1 [65.9 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 libteckit0 i386 2.5.12+ds1-1+b1 [285 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 libtexlua53-5 i386 2024.20240313.70630+ds-5+b1 [129 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libxt6t64 i386 1:1.2.1-1.2+b2 [194 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 libxmu6 i386 2:1.1.3-3+b4 [60.8 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libxpm4 i386 1:3.5.17-1+b3 [58.3 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 libxaw7 i386 2:1.0.16-1 [220 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 libxi6 i386 2:1.8.2-1 [81.2 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libzzip-0-13t64 i386 0.13.72+dfsg.1-1.2+b1 [58.1 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 t1utils i386 1.41-4 [62.3 kB]
Get: 79 http://deb.debian.org/debian trixie/main i386 tex-common all 6.18 [32.5 kB]
Get: 80 http://deb.debian.org/debian trixie/main i386 texlive-binaries i386 2024.20240313.70630+ds-5+b1 [8373 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 82 http://deb.debian.org/debian trixie/main i386 texlive-base all 2024.20250114-1 [22.8 MB]
Get: 83 http://deb.debian.org/debian trixie/main i386 texlive-latex-base all 2024.20250114-1 [1282 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 texlive-latex-recommended all 2024.20250114-1 [8760 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 78.3 MB in 1s (126 MB/s)
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(Reading database ... 19795 files and directories currently installed.)
Preparing to unpack .../00-libproc2-0_2%3a4.0.4-7_i386.deb ...
Unpacking libproc2-0:i386 (2:4.0.4-7) ...
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Unpacking procps (2:4.0.4-7) ...
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Unpacking bsdextrautils (2.40.4-3) ...
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Unpacking libpipeline1:i386 (1.5.8-1) ...
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Moving old data out of the way
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/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+dfsg1-9_source.changes
dpkg-buildpackage: info: source package velvet
dpkg-buildpackage: info: source version 1.2.10+dfsg1-9
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 (Final graph has 16 nodes and n50 of 24184, max 44966, tota
l 100080,[]
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[]\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo
s_file yes[]
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99975,[]
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g data/test_long.fa[]
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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[][]
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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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-fasta -[]
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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_
specific[]
[6]
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parameters ...)[]
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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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This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
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[] \OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, tota
l 100080,[]
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[]\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo
s_file yes[]
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[]\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon
g data/test_long.fa[]
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[3]
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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 $\OML/cmm/m/
it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 +
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[][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/
using[]openmp.htm[][]
[5]
[6]
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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so
lexa2.fa solexa3.fa -long[]
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[]\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec
ted_reads[]
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[]\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq
-fasta -[]
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[]\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_
specific[]
[7]
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arameters ...)[]
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[10]
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[]$[]$\OT1/cmr/m/n/10 . If set
[12]
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[]\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth
er parameters...)[]
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[]\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other
parameters...)[]
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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[]
[14]
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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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[16]
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[19 <./suis_plot.pdf>]
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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)
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(see the transcript file for additional information) </build/reproducible-path/
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This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
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(./Columbus_manual.tex
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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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make[2]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1'
dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/velvet-1.2.10+dfsg1'
make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1'
dh_auto_test -O--no-parallel
make -j1 test
make[1]: Entering directory '/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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;
| ^~~~~~~
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
877 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
933 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:949:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
949 | fgets(line, MAXLINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1207 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/splayTable.c:1213:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1213 | fgets(line, MAXLINE, seqFile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:970,
from src/passageMarker.c:22:
In function 'sprintf',
inlined from 'readPassageMarker' at src/passageMarker.c:291:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'readPassageMarker' at src/passageMarker.c:288:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'readPassageMarker' at src/passageMarker.c:298:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'readPassageMarker' at src/passageMarker.c:296:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin___sprintf_chk' argument 5 overlaps destination object 's' [-Wrestrict]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
In file included from /usr/include/stdio.h:970,
from src/readSet.c:22:
In function 'snprintf',
inlined from 'addMapping' at src/readSet.c:753:4,
inlined from 'readCigar' at src/readSet.c:799:6:
/usr/include/i386-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict]
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
src/readSet.c: In function 'readCigar':
src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
786 | 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 'snprintf',
inlined from 'addMapping' at src/readSet.c:751:4,
inlined from 'readCigar' at src/readSet.c:799:6:
/usr/include/i386-linux-gnu/bits/stdio2.h:68:10: warning: '__builtin___snprintf_chk' argument 6 overlaps destination object 'buffer' [-Wrestrict]
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
src/readSet.c: In function 'readCigar':
src/readSet.c:786:125: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
786 | 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:1616:25: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
1616 | strncpy(sequence + bpCount, line, lineLength);
| ^
src/readSet.c:1615:38: note: length computed here
1615 | lineLength = strlen(line) - 1;
| ^~~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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};
| ^~~~~
src/autoOpen.c: In function 'popenNoStderr':
src/autoOpen.c:28:17: warning: ignoring return value of 'dup' declared with attribute 'warn_unused_result' [-Wunused-result]
28 | dup(out[1]);
| ^~~~~~~~~~~
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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
[Wed Mar 25 06:40:40 2026] Running Velvet Test Suite
[Wed Mar 25 06:40:40 2026] Found ../velveth, ok
[Wed Mar 25 06:40:40 2026] Found ../velvetg, ok
[Wed Mar 25 06:40:40 2026] Found Sequences.31, ok
[Wed Mar 25 06:40:40 2026] Found Roadmaps.31, ok
[Wed Mar 25 06:40:40 2026] Found read1.fq.gz, ok
[Wed Mar 25 06:40:40 2026] Found read2.fq.gz, ok
[Wed Mar 25 06:40:40 2026] Found reads.fq.gz, ok
[Wed Mar 25 06:40:40 2026] Found read1.fa.gz, ok
[Wed Mar 25 06:40:40 2026] Found read2.fa.gz, ok
[Wed Mar 25 06:40:40 2026] Found reads.fa.gz, ok
[Wed Mar 25 06:40:40 2026] making test folder: velvet.test.auSWlN
[Wed Mar 25 06:40:40 2026] running test 1 of 5: fasta_eq_fastq_ascii.t
[Wed Mar 25 06:40:42 2026] ok
[Wed Mar 25 06:40:42 2026] ok
[Wed Mar 25 06:40:42 2026] ok
[Wed Mar 25 06:40:42 2026] ok
[Wed Mar 25 06:40:42 2026] passed test 1
[Wed Mar 25 06:40:42 2026] running test 2 of 5: fasta_eq_fastq_binary.t
[Wed Mar 25 06:40:44 2026] ok
[Wed Mar 25 06:40:44 2026] ok
[Wed Mar 25 06:40:44 2026] passed test 2
[Wed Mar 25 06:40:44 2026] running test 3 of 5: fmt_auto_mode.t
[Wed Mar 25 06:40:45 2026] ok
[Wed Mar 25 06:40:45 2026] ok
[Wed Mar 25 06:40:45 2026] passed test 3
[Wed Mar 25 06:40:45 2026] running test 4 of 5: interleaved_eq_separate.t
[Wed Mar 25 06:40:49 2026] ok
[Wed Mar 25 06:40:49 2026] ok
[Wed Mar 25 06:40:49 2026] passed test 4
[Wed Mar 25 06:40:49 2026] running test 5 of 5: mismatched_separates.t
[Wed Mar 25 06:40:49 2026] ok
[Wed Mar 25 06:40:49 2026] ok
[Wed Mar 25 06:40:49 2026] passed test 5
[Wed Mar 25 06:40:49 2026] removing test folder: velvet.test.auSWlN
[Wed Mar 25 06:40:49 2026] passed all 5 tests
[Wed Mar 25 06:40:49 2026] hooray!
make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1'
create-stamp debian/debhelper-build-stamp
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make[1]: Entering directory '/build/reproducible-path/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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dh_compress -X.pdf -X.c -X.pl -X.h -X.xz
make[1]: Leaving directory '/build/reproducible-path/velvet-1.2.10+dfsg1'
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dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-9_i386.deb'.
dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-9_i386.deb'.
dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-9_i386.deb'.
dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-9_i386.deb'.
dpkg-deb: building package 'velvet-example' in '../velvet-example_1.2.10+dfsg1-9_all.deb'.
dpkg-deb: building package 'velvet-tests' in '../velvet-tests_1.2.10+dfsg1-9_all.deb'.
dpkg-genbuildinfo --build=binary -O../velvet_1.2.10+dfsg1-9_i386.buildinfo
dpkg-genchanges --build=binary -O../velvet_1.2.10+dfsg1-9_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/436 and its subdirectories
I: Current time: Tue Mar 24 18:41:23 -12 2026
I: pbuilder-time-stamp: 1774420883