Sat Oct 25 21:00:31 UTC 2025 I: starting to build soapdenovo/forky/amd64 on jenkins on '2025-10-25 21:00' Sat Oct 25 21:00:31 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_20/71407/console.log Sat Oct 25 21:00:31 UTC 2025 I: Downloading source for forky/soapdenovo=1.05-7 --2025-10-25 21:00:31-- http://deb.debian.org/debian/pool/main/s/soapdenovo/soapdenovo_1.05-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2169 (2.1K) [text/prs.lines.tag] Saving to: ‘soapdenovo_1.05-7.dsc’ 0K .. 100% 212M=0s 2025-10-25 21:00:31 (212 MB/s) - ‘soapdenovo_1.05-7.dsc’ saved [2169/2169] Sat Oct 25 21:00:31 UTC 2025 I: soapdenovo_1.05-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: soapdenovo Binary: soapdenovo Architecture: any-amd64 any-ppc64 any-ia64 Version: 1.05-7 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: http://soap.genomics.org.cn/soapdenovo.html Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo Vcs-Git: https://salsa.debian.org/med-team/soapdenovo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), rename Package-List: soapdenovo deb science optional arch=any-amd64,any-ppc64,any-ia64 Checksums-Sha1: e7d8fc337de43cc6b96b2b24acbe5454cf0eadfe 377640 soapdenovo_1.05.orig.tar.gz c9c614f433c056120ed50295e3f58d04b43e8e34 608744 soapdenovo_1.05-7.debian.tar.xz Checksums-Sha256: bb2fcdc0cb2290b8d63f7afdffddf693679dbd8d6d3dd2db136a65f299794cbc 377640 soapdenovo_1.05.orig.tar.gz 523a05752e20d81ae5f02bb89704f5ad94b40cbb4c549544472a2f452f6319fe 608744 soapdenovo_1.05-7.debian.tar.xz Files: f6d16bce2b8233b6fd93c6009dcc40b3 377640 soapdenovo_1.05.orig.tar.gz 835fe9599ab03e1215403b70d0a93e02 608744 soapdenovo_1.05-7.debian.tar.xz Dgit: b8fad5a91fbbd2611b15b5fa8dfa7bffdf83d777 debian archive/debian/1.05-7 https://git.dgit.debian.org/soapdenovo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmj5TKoUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp8iRAAgAJDNkCUeNCEZdjzFx/gCb25cumY ezUMuOtZ5BwGLN2qVWeGgtK8um/RiM2cdZ19Tfwa4b1VBVRbdfwjNmn5RiAESDpt GPkUCIjeFnFwUTYQVK8zPL3zCxs0c3PLgneCtfmGmvRZFBWx+rlsVx2ThIL952xD 1HCFHbk/gj3CXAndVHVFF5KxqodV5t1irvIQL6gtNIOCJTGibf6J+3e/dlRSRVtv A6ogBD2ypXc64Hg+js+b8zJykfoVYZbHM0rxeqMYdFTbRjKkWVVuAK8gDyss2N7H CcWH94shG/McmtRbob5QZUefO8C78BN/CZMU1LHWZrLh1Gidemp6xD2HMUuUDusY ZEAgVUhTRjwDcrSprovTOuY9eF89T8DOXhGav9x1ZGaDkEnvvxUyjBI8E+RNN85u s7jysJBDGLW7fONxBMagV8E91XMtX8Gz7k5DJKSSYcODmP7DJhqo46/pm1qYKYh3 7eGXRmwzlNCewLRCNil9zI1qSQryqGmrrOtgmvi/Gt67sivwmdZD+yig2u97tR7t /NNqYz4nm8oGSdBlsHmSR8iO+awZ22wDCX6heJ3IL6dL78bF9F9UKJEBmSoXKd03 JHyD7VuAqFj8/qErXtiNg8Usmm0C6FVbRgujNHYBEuGF+Lefa02V5d2L09YDZTYT PVulylUF6zWVHVk= =8l1b -----END PGP SIGNATURE----- Sat Oct 25 21:00:31 UTC 2025 I: Checking whether the package is not for us Sat Oct 25 21:00:31 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sat Oct 25 21:00:32 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sat Oct 25 21:02:22 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 27 15:23:32 -12 2026 I: pbuilder-time-stamp: 1795836212 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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: Copying source file I: copying [soapdenovo_1.05-7.dsc] I: copying [./soapdenovo_1.05.orig.tar.gz] I: copying [./soapdenovo_1.05-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./soapdenovo_1.05-7.dsc: no acceptable signature found dpkg-source: info: extracting soapdenovo in soapdenovo-1.05 dpkg-source: info: unpacking soapdenovo_1.05.orig.tar.gz dpkg-source: info: unpacking soapdenovo_1.05-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_debug_symbols.patch dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying build-flags.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20815/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='8d8d82d7743c4ec3ace069857d5fcd36' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='20815' 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.ulwvnQt7/pbuilderrc_wPZZ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/b1 --logfile b1/build.log soapdenovo_1.05-7.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' 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 ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/20815/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19900 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 rename; however: Package rename 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} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 11.3 MB of archives. After unpacking 42.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 rename all 2.02-1 [21.8 kB] Fetched 11.3 MB in 5s (2148 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19900 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.2-1_amd64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-2_amd64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.6+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package rename. Preparing to unpack .../29-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.28) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/soapdenovo-1.05/ && 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 > ../soapdenovo_1.05-7_source.changes dpkg-buildpackage: info: source package soapdenovo dpkg-buildpackage: info: source version 1.05-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j42 clean make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' SOAPdenovo-31mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/63mer' SOAPdenovo-63mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/63mer' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/127mer' SOAPdenovo-127mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/127mer' make[1]: Leaving directory '/build/reproducible-path/soapdenovo-1.05' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j42 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' Compiling arc.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" Compiling attachPEinfo.c... Compiling bubble.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" Compiling check.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" Compiling compactEdge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" Compiling concatenateEdge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" Compiling connect.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" Compiling contig.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" Compiling cutTipPreGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" Compiling cutTip_graph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" Compiling darray.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" Compiling dfib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" Compiling dfibHeap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" Compiling fib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" Compiling fibHeap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" Compiling hashFunction.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" Compiling kmer.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" Compiling lib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" Compiling loadGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" Compiling loadPath.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" Compiling loadPreGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" Compiling localAsm.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" Compiling main.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" Compiling map.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" Compiling mem_manager.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" Compiling newhash.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" Compiling node2edge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" Compiling orderContig.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" Compiling output_contig.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" Compiling output_pregraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" Compiling output_scaffold.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" Compiling pregraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" Compiling prlHashCtg.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" Compiling prlHashReads.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" Compiling prlRead2Ctg.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" Compiling prlRead2path.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" Compiling prlReadFillGap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" Compiling read2scaf.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" Compiling readInterval.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" Compiling stack.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" Compiling readseq1by1.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" Compiling scaffold.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" loadPath.c: In function 'loadPath': loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 58 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c: In function 'loadPathBin': loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 164 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 168 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ attachPEinfo.c: In function 'loadPEgrads': attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | fgets ( line, sizeof ( line ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c: In function 'basicContigInfo': prlRead2Ctg.c:494:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 494 | fgets ( lldne, sizeof ( lldne ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c:499:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 499 | fgets ( lldne, sizeof ( lldne ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ map.c: In function 'getMinOverlap.constprop': map.c:40:28: warning: '.preGraphBasic' directive writing 14 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 40 | sprintf ( name, "%s.preGraphBasic", gfile ); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from inc/stdinc.h:24, from map.c:23: In function 'sprintf', inlined from 'getMinOverlap.constprop' at map.c:40:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ loadGraph.c: In function 'loadUpdatedVertex': loadGraph.c:57:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf ( fp, "%llx ", &word ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadPreGraph.c: In function 'loadVertex': loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 77 | fscanf ( fp, "%llx ", &word ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseq1by1.c: In function 'read1seqfq': readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 213 | fgets ( str, 4950, fp ); // pass quality value line | ^~~~~~~~~~~~~~~~~~~~~~~ read2scaf.c: In function 'locateReadOnScaf': read2scaf.c:282:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fgets ( line, 1024, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ orderContig.c: In function 'PE2Links': orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2765 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ orderContig.c: In function 'Links2Scaf': orderContig.c:2891:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2891 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ Compiling searchPath.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" Compiling seq.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" Compiling splitReps.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -Wl,-z,relro -Wl,-z,now -o SOAPdenovo-31mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o localAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o -pthread -lm Linking... SOAPdenovo-31mer compilation done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/63mer' Compiling arc.c... Compiling attachPEinfo.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" Compiling bubble.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" Compiling check.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" Compiling compactEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" Compiling concatenateEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" Compiling connect.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" Compiling contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" Compiling cutTipPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" Compiling cutTip_graph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" Compiling darray.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" Compiling dfib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" Compiling dfibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" Compiling fib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" Compiling fibHeap.c... Compiling hashFunction.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" Compiling kmer.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" Compiling lib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" Compiling loadGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" Compiling loadPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" Compiling loadPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" Compiling localAsm.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" Compiling main.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" Compiling map.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" Compiling mem_manager.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" Compiling newhash.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" Compiling node2edge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" Compiling orderContig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" Compiling output_contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" Compiling output_pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" Compiling output_scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" Compiling pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" Compiling prlHashCtg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" Compiling prlHashReads.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" Compiling prlRead2Ctg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" Compiling prlRead2path.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" Compiling prlReadFillGap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" Compiling read2scaf.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" Compiling readInterval.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" Compiling stack.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" Compiling readseq1by1.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" Compiling scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" attachPEinfo.c: In function 'loadPEgrads': attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | fgets ( line, sizeof ( line ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Compiling searchPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" read2scaf.c: In function 'locateReadOnScaf': read2scaf.c:286:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets ( line, 1024, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ readseq1by1.c: In function 'read1seqfq': readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 213 | fgets ( str, 4950, fp ); // pass quality value line | ^~~~~~~~~~~~~~~~~~~~~~~ Compiling seq.c... loadPath.c: In function 'loadPath': loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 58 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c: In function 'loadPathBin': loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 164 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 168 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" map.c: In function 'getMinOverlap.constprop': map.c:40:28: warning: '.preGraphBasic' directive writing 14 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 40 | sprintf ( name, "%s.preGraphBasic", gfile ); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from inc/stdinc.h:24, from map.c:23: In function 'sprintf', inlined from 'getMinOverlap.constprop' at map.c:40:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Compiling splitReps.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" orderContig.c: In function 'PE2Links': orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2765 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ orderContig.c: In function 'Links2Scaf': orderContig.c:2890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2890 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c: In function 'basicContigInfo': prlRead2Ctg.c:493:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 493 | fgets ( lldne, sizeof ( lldne ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c:498:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 498 | fgets ( lldne, sizeof ( lldne ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadPreGraph.c: In function 'loadVertex': loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 77 | fscanf ( fp, "%llx %llx", & ( word.high ), & ( word.low ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -Wl,-z,relro -Wl,-z,now -o SOAPdenovo-63mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o localAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o -pthread -lm Linking... SOAPdenovo-63mer compilation done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/63mer' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/127mer' Compiling arc.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" Compiling attachPEinfo.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" Compiling bubble.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" Compiling check.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" Compiling compactEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" Compiling concatenateEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" Compiling connect.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" Compiling contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" Compiling cutTipPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" Compiling cutTip_graph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" Compiling darray.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" Compiling dfib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" Compiling dfibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" Compiling fib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" Compiling fibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" Compiling hashFunction.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" Compiling kmer.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" Compiling lib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" Compiling loadGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" Compiling loadPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" Compiling loadPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" Compiling localAsm.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" Compiling main.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" Compiling map.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" Compiling mem_manager.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" Compiling newhash.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" Compiling node2edge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" Compiling orderContig.c... Compiling output_contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" Compiling output_pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" Compiling output_scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" Compiling pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" Compiling prlHashCtg.c... Compiling prlHashReads.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" Compiling prlRead2Ctg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" Compiling prlRead2path.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" Compiling prlReadFillGap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" Compiling read2scaf.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" Compiling readInterval.c... Compiling stack.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" Compiling readseq1by1.c... Compiling scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" attachPEinfo.c: In function 'loadPEgrads': attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | fgets ( line, sizeof ( line ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Compiling searchPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" Compiling seq.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" loadPath.c: In function 'loadPath': loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 58 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c: In function 'loadPathBin': loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 164 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 168 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ Compiling splitReps.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" map.c: In function 'getMinOverlap.constprop': map.c:40:28: warning: '.preGraphBasic' directive writing 14 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 40 | sprintf ( name, "%s.preGraphBasic", gfile ); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from inc/stdinc.h:24, from map.c:23: In function 'sprintf', inlined from 'getMinOverlap.constprop' at map.c:40:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ orderContig.c: In function 'PE2Links': read2scaf.c: In function 'locateReadOnScaf': read2scaf.c:286:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets ( line, 1024, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2765 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c: In function 'basicContigInfo': orderContig.c: In function 'Links2Scaf': orderContig.c:2890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2890 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c:493:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 493 | fgets ( lldne, sizeof ( lldne ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prlRead2Ctg.c:498:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 498 | fgets ( lldne, sizeof ( lldne ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadPreGraph.c: In function 'loadVertex': loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 77 | fscanf ( fp, "%llx %llx %llx %llx", & ( word.high1 ), & ( word.low1 ), & ( word.high2 ), & ( word.low2 ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseq1by1.c: In function 'read1seqfq': readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 213 | fgets ( str, 4950, fp ); // pass quality value line | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -Wl,-z,relro -Wl,-z,now -o SOAPdenovo-127mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o localAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o -pthread -lm Linking... SOAPdenovo-127mer compilation done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/127mer' Installation done. make[1]: Leaving directory '/build/reproducible-path/soapdenovo-1.05' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/soapdenovo/ make -j42 install DESTDIR=/build/reproducible-path/soapdenovo-1.05/debian/soapdenovo AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' Installation done. make[1]: Leaving directory '/build/reproducible-path/soapdenovo-1.05' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' dh_install cd debian/soapdenovo/usr/bin/;rename 's/SOAP/soap/' SOAP* make[1]: Leaving directory '/build/reproducible-path/soapdenovo-1.05' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'soapdenovo-dbgsym' in '../soapdenovo-dbgsym_1.05-7_amd64.deb'. dpkg-deb: building package 'soapdenovo' in '../soapdenovo_1.05-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../soapdenovo_1.05-7_amd64.buildinfo dpkg-genchanges --build=binary -O../soapdenovo_1.05-7_amd64.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/20815 and its subdirectories I: Current time: Fri Nov 27 15:25:21 -12 2026 I: pbuilder-time-stamp: 1795836321 Sat Oct 25 21:02:22 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Sat Oct 25 21:02:22 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Sat Oct 25 21:05:16 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Sat Oct 25 21:05:16 UTC 2025 I: soapdenovo_1.05-7_amd64.changes: Format: 1.8 Date: Wed, 22 Oct 2025 23:26:00 +0200 Source: soapdenovo Binary: soapdenovo soapdenovo-dbgsym Architecture: amd64 Version: 1.05-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: soapdenovo - short-read assembly method to build de novo draft assembly Closes: 1097907 Changes: soapdenovo (1.05-7) unstable; urgency=medium . * Team upload. * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097907) * d/watch: convert to untrackable watch file v5. * build-flags.patch: new: propagate build flags. This notably fixes missing binaries hardening. * add_debug_symbols.patch: normalize Last-Update timestamp. * d/control: drop redundant Rules-Requires-Root: no. * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: 7daa9f5a5a28a0b5142895fa162cd65fb3cef461 1004028 soapdenovo-dbgsym_1.05-7_amd64.deb 087a3d2790e4c27a3f30b798221bdc64da9d81dd 4859 soapdenovo_1.05-7_amd64.buildinfo d26a9081bb82c05966475a459b610d6b70095d3f 946112 soapdenovo_1.05-7_amd64.deb Checksums-Sha256: 943e2a5206cf78fdbde29e4817c57fbf2f154a6fafe1f5493ba4c71a365cbb8b 1004028 soapdenovo-dbgsym_1.05-7_amd64.deb efa429a3b46873e91211652f8134b5e8984f3a8edc436a85e97e70649413b18d 4859 soapdenovo_1.05-7_amd64.buildinfo 74eef53b0aefbd8c2ed36b497a1856359d94757f55108cd9668b5195a334745e 946112 soapdenovo_1.05-7_amd64.deb Files: 9c6bc3426478ddb4a8dfa8320ef09327 1004028 debug optional soapdenovo-dbgsym_1.05-7_amd64.deb 93908ca8aeb4d60789446748dcd6172f 4859 science optional soapdenovo_1.05-7_amd64.buildinfo db5294dc9440c213fead80ba5b083cc7 946112 science optional soapdenovo_1.05-7_amd64.deb Sat Oct 25 21:05:17 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_20-71407.service; invocation ID: 8764f363e8644270a62a47734e5fdf62 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/soapdenovo_1.05-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/soapdenovo_1.05-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/soapdenovo_1.05-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/b1/soapdenovo_1.05-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/b2/soapdenovo_1.05-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 205ms CPU time consumed: 176ms Memory peak: 17.9M (swap: 0B) Sat Oct 25 21:14:25 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Sat Oct 25 21:14:25 UTC 2025 I: soapdenovo from forky built successfully and reproducibly on amd64. Sat Oct 25 21:14:26 UTC 2025 I: Removing signed soapdenovo_1.05-7_amd64.buildinfo.asc files: removed './b1/soapdenovo_1.05-7_amd64.buildinfo.asc' removed './b2/soapdenovo_1.05-7_amd64.buildinfo.asc'