Wed Nov 27 00:55:56 UTC 2024 I: starting to build spades/experimental/amd64 on jenkins on '2024-11-27 00:55' Wed Nov 27 00:55:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/40645/console.log Wed Nov 27 00:55:56 UTC 2024 I: Downloading source for experimental/spades=4.0.0+dfsg1-1 --2024-11-27 00:55:56-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/spades/spades_4.0.0%2bdfsg1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2521 (2.5K) [text/prs.lines.tag] Saving to: ‘spades_4.0.0+dfsg1-1.dsc’ 0K .. 100% 295M=0s 2024-11-27 00:55:56 (295 MB/s) - ‘spades_4.0.0+dfsg1-1.dsc’ saved [2521/2521] Wed Nov 27 00:55:56 UTC 2024 I: spades_4.0.0+dfsg1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: spades Binary: spades Architecture: amd64 Version: 4.0.0+dfsg1-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss , Michael R. Crusoe , Alexandre Mestiashvili , Étienne Mollier Homepage: https://github.com/ablab/spades Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/spades Vcs-Git: https://salsa.debian.org/med-team/spades.git Testsuite: autopkgtest Testsuite-Triggers: bwa Build-Depends: debhelper-compat (= 13), dh-sequence-python3, asciidoctor, clang-format, clang-tidy, clang-tools, cmake, libbam-dev, libbamtools-dev, libbz2-dev, libboost-thread-dev, libc++-dev, libcuckoo-dev, libgtest-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libparallel-hashmap-dev, libspoa-dev, libssw-dev, libxxhash-dev, libzstd-dev, llvm-dev, lynx, python3-all, python3-joblib, python3-yaml, zlib1g-dev Package-List: spades deb science optional arch=amd64 Checksums-Sha1: feda8783c3544227edbe3537798411d570095b6a 9961224 spades_4.0.0+dfsg1.orig.tar.xz ad166fbf6a5fe9a1ba63c4a2931377a095e4e532 40372 spades_4.0.0+dfsg1-1.debian.tar.xz Checksums-Sha256: b3634165e29be26856f0ccaa1bac5b140747d744419b475ffea0a7f1df4e7a5a 9961224 spades_4.0.0+dfsg1.orig.tar.xz 94d2a205c9bf7ec93b59bf409de5cb91179553ae4927e8563420678a0484eb73 40372 spades_4.0.0+dfsg1-1.debian.tar.xz Files: 962bfd8677abfde9ee7856f048ea06a6 9961224 spades_4.0.0+dfsg1.orig.tar.xz 2bc5f0897e5c0b09abc6b6f21d64aee3 40372 spades_4.0.0+dfsg1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmb870sACgkQYAMWptwn dHZIkA/+LKAHBkumAR/bMcIiScQeRCoup8naE0YPKQH+wspVTXbqhlTRLDllqloL lMDgf+2DxrJ8/tgKqiSZrOM4taeYGKJ5aDsi3B8EKmRMJ4yiweJj3YSyTjdRc2Ui ysgWgpWxLy7qzistG4ohSb9Fn59nAsC5lzitMl4eR6zTEZqF30XJPN8Rgz4f9fUR LPQyKmhGwK0+49s4/UVfNRoUh6770vvkJ06zOVLUV8GK78rYgyMgpF9V8xlsBSLc nXYsmJPExgNC4m1zGI5+UiKTj4FCd5XO+iokAJAN+P4NkN8mfdBi3eV96CHjVF9K ZpLSqVo6o/X3KRvh33IYii9wcoN63DRcnnQIlf4iXDdRf9IcHgTgxNzlgBlAEzoo PK4PHUZupAg9IzLL2RqMzqMtGoEhsJADDyOmSjDYixB4Ru0wzxaxcOJdrqE2oGAt bSEYBgtiajeaI9ly4oY7vKa/fStnbYCEJvS1za9AFyt6mP1uqVYxGnFsma4HH7me pvsmQndFaiCpXQQXvy0jk5anJnrSsWn2uvbAnnQsMpfLa8w8fPt3iLJL9t0kw1cG KTkxGFjBJ8LRoGn8OxQUmzEHJHNEM3tAg4NWi8b+d2yL+yN89Xjx62u3LqEz6+Ue eX1HB45WzpBttF8NcXaZaEDim8ub2Ta4rDZdB9Tef2ddg52nz2M= =CFUS -----END PGP SIGNATURE----- Wed Nov 27 00:55:56 UTC 2024 I: Checking whether the package is not for us Wed Nov 27 00:55:56 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Wed Nov 27 00:55:56 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Wed Nov 27 01:04:14 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 29 19:18:57 -12 2025 I: pbuilder-time-stamp: 1767079137 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [spades_4.0.0+dfsg1-1.dsc] I: copying [./spades_4.0.0+dfsg1.orig.tar.xz] I: copying [./spades_4.0.0+dfsg1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 2 06:59:23 2024 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./spades_4.0.0+dfsg1-1.dsc: no acceptable signature found dpkg-source: info: extracting spades in spades-4.0.0+dfsg1 dpkg-source: info: unpacking spades_4.0.0+dfsg1.orig.tar.xz dpkg-source: info: unpacking spades_4.0.0+dfsg1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 0101_cmake_ignore_removed_python-yaml.patch dpkg-source: info: applying 0102_cmake_ignore_removed_python-joblib.patch dpkg-source: info: applying bamtools-cmake.patch dpkg-source: info: applying 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying python3.patch dpkg-source: info: applying yaml_load.patch dpkg-source: info: applying debuginfo.patch dpkg-source: info: applying debian_bwa_zlib.patch dpkg-source: info: applying workdir_for_test.patch dpkg-source: info: applying disable_local_convertutf.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying use_debian_xxhash.patch dpkg-source: info: applying use_debian_cuckoo.patch dpkg-source: info: applying samtools_missing_source.patch dpkg-source: info: applying deactivate_tests_with_no_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3850233/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='experimental' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='60926e714fd448e085d8eb2a87e0d27c' 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='3850233' 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.1zOzKOYZ/pbuilderrc_aBG9 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1zOzKOYZ/b1 --logfile b1/build.log spades_4.0.0+dfsg1-1.dsc' SUDO_GID='111' 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 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3850233/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), dh-sequence-python3, asciidoctor, clang-format, clang-tidy, clang-tools, cmake, libbam-dev, libbamtools-dev, libbz2-dev, libboost-thread-dev, libc++-dev, libcuckoo-dev, libgtest-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libparallel-hashmap-dev, libspoa-dev, libssw-dev, libxxhash-dev, libzstd-dev, llvm-dev, lynx, python3-all, python3-joblib, python3-yaml, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19973 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on clang-format; however: Package clang-format is not installed. pbuilder-satisfydepends-dummy depends on clang-tidy; however: Package clang-tidy is not installed. pbuilder-satisfydepends-dummy depends on clang-tools; however: Package clang-tools is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libc++-dev; however: Package libc++-dev is not installed. pbuilder-satisfydepends-dummy depends on libcuckoo-dev; however: Package libcuckoo-dev is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libparallel-hashmap-dev; however: Package libparallel-hashmap-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libxxhash-dev; however: Package libxxhash-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on llvm-dev; however: Package llvm-dev is not installed. pbuilder-satisfydepends-dummy depends on lynx; however: Package lynx is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} clang-19{a} clang-format{a} clang-format-19{a} clang-tidy{a} clang-tidy-19{a} clang-tools{a} clang-tools-19{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.2{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libc++-19-dev{a} libc++-dev{a} libc++1-19{a} libc++abi-19-dev{a} libc++abi1-19{a} libcereal-dev{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcuckoo-dev{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libgc1{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} libllvm19{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libnsl2{a} libobjc-14-dev{a} libobjc4{a} libp11-kit-dev{a} libparallel-hashmap-dev{a} libpfm4{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libunwind-19{a} libunwind-19-dev{a} libuv1t64{a} libxml2{a} libxml2-dev{a} libxxhash-dev{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzstd-dev{a} llvm{a} llvm-19{a} llvm-19-dev{a} llvm-19-linker-tools{a} llvm-19-runtime{a} llvm-19-tools{a} llvm-dev{a} llvm-runtime{a} lynx{a} lynx-common{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-joblib{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-pygments{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} rake{a} rapidjson-dev{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support bzip2-doc fonts-lato krb5-locales libarchive-cpio-perl libclang-rt-19-dev libgpm2 libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults mailcap psmisc publicsuffix python3-numpy python3-psutil python3-pytest python3-simplejson systemd zip 0 packages upgraded, 222 newly installed, 0 to remove and 0 not upgraded. Need to get 238 MB of archives. After unpacking 1353 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.0-2 [856 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.0-2 [2038 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.3-2 [26.0 MB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.3-2 [13.2 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libobjc4 amd64 14.2.0-8 [42.5 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libobjc-14-dev amd64 14.2.0-8 [170 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libclang-common-19-dev amd64 1:19.1.3-2 [739 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.3-2 [1260 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.3-2 [7622 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 clang-19 amd64 1:19.1.3-2 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 clang-format-19 amd64 1:19.1.3-2 [91.9 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 clang-format amd64 1:19.0-63 [6352 B] Get: 74 http://deb.debian.org/debian unstable/main amd64 clang-tools-19 amd64 1:19.1.3-2 [8950 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 clang-tidy-19 amd64 1:19.1.3-2 [1882 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 clang-tidy amd64 1:19.0-63 [6116 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 clang-tools amd64 1:19.0-63 [6164 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.1-1 [2267 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.1-1 [11.9 MB] Get: 94 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.1-1+b1 [54.8 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 101 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 googletest all 1.15.2-1 [514 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3.2+b1 [10.6 MB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3.2+b1 [234 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3.2+b1 [235 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-3.2+b1 [240 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-3.2+b1 [246 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-3.2+b1 [230 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3.2+b1 [334 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3.2+b1 [373 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-3.2+b1 [239 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-3.2+b1 [230 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-3.2+b1 [232 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2+b1 [269 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-3.2+b1 [277 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libunwind-19 amd64 1:19.1.3-2 [62.2 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libc++abi1-19 amd64 1:19.1.3-2 [105 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libc++1-19 amd64 1:19.1.3-2 [302 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libc++abi-19-dev amd64 1:19.1.3-2 [127 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libunwind-19-dev amd64 1:19.1.3-2 [80.7 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libc++-19-dev amd64 1:19.1.3-2 [1285 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libc++-dev amd64 1:19.0-63 [6056 B] Get: 153 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libcuckoo-dev all 0.3.1-3 [37.5 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-1 [64.9 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-1 [88.3 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1 [472 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.15.2-1 [259 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-6+b1 [178 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libnlopt-dev amd64 2.7.1-6+b1 [46.8 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx0 amd64 2.7.1-6+b1 [205 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx-dev amd64 2.7.1-6+b1 [13.5 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libparallel-hashmap-dev all 1.4.1+ds-1 [205 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [1992 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libspoa-dev amd64 4.1.4-2+b1 [9808 B] Get: 205 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b1 [21.8 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b1 [24.6 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libxxhash-dev amd64 0.8.2-2+b2 [79.4 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.13.3-1 [107 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.3-2 [550 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 llvm-runtime amd64 1:19.0-63 [5904 B] Get: 212 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.3-2 [16.4 MB] Get: 213 http://deb.debian.org/debian unstable/main amd64 llvm amd64 1:19.0-63 [8328 B] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 llvm-19-tools amd64 1:19.1.3-2 [510 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 llvm-19-dev amd64 1:19.1.3-2 [43.2 MB] Get: 217 http://deb.debian.org/debian unstable/main amd64 llvm-dev amd64 1:19.0-63 [6152 B] Get: 218 http://deb.debian.org/debian unstable/main amd64 lynx-common all 2.9.2-1 [1193 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.0-2 [730 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-5 [216 kB] Fetched 238 MB in 3s (83.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19973 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20293 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (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 ... 21355 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. 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Preparing to unpack .../050-clang-format-19_1%3a19.1.3-2_amd64.deb ... Unpacking clang-format-19 (1:19.1.3-2) ... Selecting previously unselected package clang-format:amd64. Preparing to unpack .../051-clang-format_1%3a19.0-63_amd64.deb ... Unpacking clang-format:amd64 (1:19.0-63) ... Selecting previously unselected package clang-tools-19. Preparing to unpack .../052-clang-tools-19_1%3a19.1.3-2_amd64.deb ... Unpacking clang-tools-19 (1:19.1.3-2) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../053-python3-yaml_6.0.2-1+b1_amd64.deb ... Unpacking python3-yaml (6.0.2-1+b1) ... Selecting previously unselected package clang-tidy-19. Preparing to unpack .../054-clang-tidy-19_1%3a19.1.3-2_amd64.deb ... Unpacking clang-tidy-19 (1:19.1.3-2) ... Selecting previously unselected package clang-tidy. Preparing to unpack .../055-clang-tidy_1%3a19.0-63_amd64.deb ... Unpacking clang-tidy (1:19.0-63) ... Selecting previously unselected package clang-tools:amd64. 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Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.8-2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libboost-date-time1.83.0:amd64 (1.83.0-3.2+b1) ... Setting up libunwind-19:amd64 (1:19.1.3-2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libclang-common-19-dev:amd64 (1:19.1.3-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libboost-system1.83.0:amd64 (1.83.0-3.2+b1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... 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Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up python3.13-minimal (3.13.0-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up cmake-data (3.31.1-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up lynx (2.9.2-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libunwind-19-dev:amd64 (1:19.1.3-2) ... Setting up libnlopt-dev:amd64 (2.7.1-6+b1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up openssl (3.3.2-2) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up libssw0:amd64 (1.1-15+b1) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:amd64 (72.1-5+b1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libllvm19:amd64 (1:19.1.3-2) ... Setting up libz3-dev:amd64 (4.13.3-1) ... Setting up libncurses-dev:amd64 (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up libclang1-19 (1:19.1.3-2) ... Setting up libboost-chrono1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libgtest-dev:amd64 (1.15.2-1) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libc++abi-19-dev:amd64 (1:19.1.3-2) ... Setting up libssw-dev:amd64 (1.1-15+b1) ... Setting up libtool (2.4.7-8) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libcereal-dev (1.3.2+dfsg-5) ... Setting up libobjc4:amd64 (14.2.0-8) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libobjc-14-dev:amd64 (14.2.0-8) ... Setting up libngtcp2-dev:amd64 (1.9.1-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up libc++-19-dev:amd64 (1:19.1.3-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libnlopt-cxx-dev:amd64 (2.7.1-6+b1) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libboost-date-time1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libldap-dev:amd64 (2.5.18+dfsg-3+b1) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-6+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up llvm-19-linker-tools (1:19.1.3-2) ... Setting up llvm-19-runtime (1:19.1.3-2) ... Setting up libc++-dev:amd64 (1:19.0-63) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... Setting up libclang-cpp19 (1:19.1.3-2) ... Setting up libboost-thread1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libspoa-dev:amd64 (4.1.4-2+b1) ... Setting up python3.13 (3.13.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up clang-19 (1:19.1.3-2) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up llvm-runtime:amd64 (1:19.0-63) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.31.1-1) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up llvm-19 (1:19.1.3-2) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up llvm (1:19.0-63) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up clang-tools-19 (1:19.1.3-2) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up clang-tools:amd64 (1:19.0-63) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up clang-format-19 (1:19.1.3-2) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up clang-format:amd64 (1:19.0-63) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-joblib (1.3.2-5) ... Setting up clang-tidy-19 (1:19.1.3-2) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up llvm-19-tools (1:19.1.3-2) ... Setting up dh-python (6.20241024) ... Setting up clang-tidy (1:19.0-63) ... Setting up llvm-19-dev (1:19.1.3-2) ... Setting up llvm-dev (1:19.0-63) ... Setting up rake (13.2.1-1) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/spades-4.0.0+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_4.0.0+dfsg1-1_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 4.0.0+dfsg1-1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_clean find . -name "*.pyc" -delete rm -rf /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.html /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.? rm -rf /build/reproducible-path/spades-4.0.0+dfsg1/debian/man make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_autoreconf_clean -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_clean -X.orig make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' debian/rules binary dh binary --sourcedirectory=src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_configure -- -DBoost_NO_BOOST_CMAKE=TRUE -DSPADES_BOOST_ROOT:PATH="/usr" cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBoost_NO_BOOST_CMAKE=TRUE -DSPADES_BOOST_ROOT:PATH=/usr ../src -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found bamtools: /usr/lib/x86_64-linux-gnu/libbamtools.so -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so - found CMake Warning (dev) at cmake/deps.cmake:29 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable BOOST_ROOT is set to: SPADES_BOOST_ROOT For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. Call Stack (most recent call first): CMakeLists.txt:66 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/deps.cmake:29 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:66 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/include (found version "1.83.0") Making Release Configuration... -- Building SPAdes version 4.0.0 Building SPAdes from N/A, sha: N/A CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- -- Override standard malloc (MI_OVERRIDE=ON) -- Enable abort() calls on memory allocation failure (MI_XMALLOC=ON) -- Enable printing of error and warning messages by default (MI_SHOW_ERRORS=ON) -- Use the C++ compiler to compile (MI_USE_CXX=ON) -- -- Library base name: mimalloc -- Version : 2.0 -- Build type : none -- C++ Compiler : /usr/bin/c++ -- Compiler flags : -Wall;-Wextra;-Wno-unknown-pragmas;-fvisibility=hidden;-ftls-model=initial-exec;-fno-builtin-malloc -- Compiler defines : MI_XMALLOC=1;MI_SHOW_ERRORS=1 -- Link libraries : /usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a -- Build targets : object -- CMake Warning (dev) at /usr/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): Calling FetchContent_Populate(zlib_ng) is deprecated, call FetchContent_MakeAvailable(zlib_ng) instead. Policy CMP0169 can be set to OLD to allow FetchContent_Populate(zlib_ng) to be called directly for now, but the ability to call it with declared details will be removed completely in a future version. Call Stack (most recent call first): /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/CMakeLists.txt:20 (FetchContent_Populate) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Using CMake version 3.31.1 -- ZLIB_HEADER_VERSION: 1.3.0 -- ZLIBNG_HEADER_VERSION: 2.1.4 -- Arch detected: 'x86_64' -- Basearch of 'x86_64' has been detected as: 'x86' -- Performing Test FNO_LTO_AVAILABLE -- Performing Test FNO_LTO_AVAILABLE - Success -- Looking for arm_acle.h -- Looking for arm_acle.h - not found -- Looking for sys/auxv.h -- Looking for sys/auxv.h - found -- Looking for sys/sdt.h -- Looking for sys/sdt.h - not found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for strerror -- Looking for strerror - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for aligned_alloc -- Looking for aligned_alloc - found -- Performing Test HAVE_NO_INTERPOSITION -- Performing Test HAVE_NO_INTERPOSITION - Success -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_HIDDEN -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_HIDDEN - Success -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_INTERNAL -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_INTERNAL - Success -- Performing Test HAVE_ATTRIBUTE_ALIGNED -- Performing Test HAVE_ATTRIBUTE_ALIGNED - Success -- Performing Test HAVE_THREAD_LOCAL -- Performing Test HAVE_THREAD_LOCAL - Success -- Performing Test HAVE_BUILTIN_CTZ -- Performing Test HAVE_BUILTIN_CTZ - Success -- Performing Test HAVE_BUILTIN_CTZLL -- Performing Test HAVE_BUILTIN_CTZLL - Success -- Performing Test HAVE_PTRDIFF_T -- Performing Test HAVE_PTRDIFF_T - Success -- Performing Test HAVE_AVX2_INTRIN -- Performing Test HAVE_AVX2_INTRIN - Success -- Performing Test HAVE_CASCADE_LAKE -- Performing Test HAVE_CASCADE_LAKE - Success -- Performing Test HAVE_AVX512_INTRIN -- Performing Test HAVE_AVX512_INTRIN - Success -- Performing Test HAVE_MASK_INTRIN -- Performing Test HAVE_MASK_INTRIN - Success -- Performing Test HAVE_AVX512VNNI_INTRIN -- Performing Test HAVE_AVX512VNNI_INTRIN - Success -- Performing Test HAVE_SSE42_INTRIN -- Performing Test HAVE_SSE42_INTRIN - Success -- Performing Test HAVE_SSE2_INTRIN -- Performing Test HAVE_SSE2_INTRIN - Success -- Performing Test HAVE_SSSE3_INTRIN -- Performing Test HAVE_SSSE3_INTRIN - Success -- Performing Test HAVE_PCLMULQDQ_INTRIN -- Performing Test HAVE_PCLMULQDQ_INTRIN - Success -- Performing Test HAVE_VPCLMULQDQ_INTRIN -- Performing Test HAVE_VPCLMULQDQ_INTRIN - Success -- Performing Test HAVE_XSAVE_INTRIN -- Performing Test HAVE_XSAVE_INTRIN - Success -- Architecture-specific source files: arch/x86/x86_features.c;arch/x86/slide_hash_avx2.c;arch/x86/chunkset_avx2.c;arch/x86/compare256_avx2.c;arch/x86/adler32_avx2.c;arch/x86/adler32_avx512.c;arch/x86/adler32_avx512_vnni.c;arch/x86/adler32_sse42.c;arch/x86/insert_string_sse42.c;arch/x86/chunkset_sse2.c;arch/x86/compare256_sse2.c;arch/x86/slide_hash_sse2.c;arch/x86/adler32_ssse3.c;arch/x86/chunkset_ssse3.c;arch/x86/crc32_pclmulqdq.c;arch/x86/crc32_vpclmulqdq.c CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/test/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The following features have been enabled: * CMAKE_BUILD_TYPE, Build type: None (selected) * AVX2_SLIDEHASH, Support AVX2 optimized slide_hash, using "-mavx2" * AVX2_CHUNKSET, Support AVX2 optimized chunkset, using "-mavx2" * AVX2_COMPARE256, Support AVX2 optimized compare256, using "-mavx2" * AVX2_ADLER32, Support AVX2-accelerated adler32, using "-mavx2" * AVX512_ADLER32, Support AVX512-accelerated adler32, using "-mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake" * AVX512VNNI_ADLER32, Support AVX512VNNI adler32, using "-mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake" * SSE42_CRC, Support SSE4.2 optimized CRC hash generation, using "-msse4.2" * SSSE3_ADLER32, Support SSSE3-accelerated adler32, using "-mssse3" * PCLMUL_CRC, Support CRC hash generation using PCLMULQDQ, using "-mssse3 -msse4.2 -mpclmul" * VPCLMUL_CRC, Support CRC hash generation using VPCLMULQDQ, using "-mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake" * XSAVE, Support XSAVE intrinsics using "-mxsave" * WITH_GZFILEOP, Compile with support for gzFile related functions * ZLIB_COMPAT, Compile with zlib compatible API * ZLIB_ENABLE_TESTS, Build test binaries * ZLIBNG_ENABLE_TESTS, Test zlib-ng specific API * WITH_SANITIZER, Enable sanitizer support * WITH_OPTIM, Build with optimisation * WITH_NEW_STRATEGIES, Use new strategies * WITH_AVX2, Build with AVX2 * WITH_AVX512, Build with AVX512 * WITH_AVX512VNNI, Build with AVX512 VNNI * WITH_SSE2, Build with SSE2 * WITH_SSSE3, Build with SSSE3 * WITH_SSE42, Build with SSE42 * WITH_PCLMULQDQ, Build with PCLMULQDQ * WITH_VPCLMULQDQ, Build with VPCLMULQDQ -- The following OPTIONAL packages have been found: * bamtools * OpenMP * Curses -- The following REQUIRED packages have been found: * BZip2 * Boost -- The following features have been disabled: * ZLIB_SYMBOL_PREFIX, Publicly exported symbols DO NOT have a custom prefix * WITH_GTEST, Build gtest_zlib * WITH_FUZZERS, Build test/fuzz * WITH_BENCHMARKS, Build test/benchmarks * WITH_BENCHMARK_APPS, Build application benchmarks * WITH_NATIVE_INSTRUCTIONS, Instruct the compiler to use the full instruction set on this host (gcc/clang -march=native) * WITH_MAINTAINER_WARNINGS, Build with project maintainer warnings * WITH_CODE_COVERAGE, Enable code coverage reporting * WITH_INFLATE_STRICT, Build with strict inflate distance checking * WITH_INFLATE_ALLOW_INVALID_DIST, Build with zero fill for inflate invalid distances * INSTALL_UTILS, Copy minigzip and minideflate during install -- The following OPTIONAL packages have not been found: * Readline -- Looking for open -- Looking for open - found -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for cxxabi.h -- Looking for cxxabi.h - not found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for mach/mach.h -- Looking for mach/mach.h - not found -- Looking for link.h -- Looking for link.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for malloc/malloc.h -- Looking for malloc/malloc.h - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Looking for futimens -- Looking for futimens - found -- Looking for futimes -- Looking for futimes - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for mallinfo -- Looking for mallinfo - found -- Looking for mallctl -- Looking for mallctl - not found -- Looking for malloc_zone_statistics -- Looking for malloc_zone_statistics - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Looking for pthread_getspecific in pthread -- Looking for pthread_getspecific in pthread - found -- Looking for pthread_rwlock_init in pthread -- Looking for pthread_rwlock_init in pthread - found -- Looking for pthread_mutex_lock in pthread -- Looking for pthread_mutex_lock in pthread - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Performing Test HAVE_FFI_CALL -- Performing Test HAVE_FFI_CALL - Success -- Found FFI: /usr/lib/x86_64-linux-gnu/libffi.so -- Could NOT find LibEdit (missing: LibEdit_INCLUDE_DIRS LibEdit_LIBRARIES) -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found zstd: /usr/lib/x86_64-linux-gnu/libzstd.so -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.11.0") -- Looking for shm_open -- Looking for shm_open - found CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for include file endian.h -- Looking for include file endian.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Looking for include file sys/param.h -- Looking for include file sys/param.h - found -- Looking for include file sys/sysctl.h -- Looking for include file sys/sysctl.h - not found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Performing Test eslENABLE_SSE -- Performing Test eslENABLE_SSE - Success -- Performing Test eslENABLE_SSE4 -- Performing Test eslENABLE_SSE4 - Failed -- Performing Test eslENABLE_AVX -- Performing Test eslENABLE_AVX - Failed -- Performing Test eslENABLE_AVX512 -- Performing Test eslENABLE_AVX512 - Failed -- Performing Test eslENABLE_NEON -- Performing Test eslENABLE_NEON - Failed -- Performing Test eslHAVE_NEON_AARCH64 -- Performing Test eslHAVE_NEON_AARCH64 - Failed -- Performing Test HAVE_FLUSH_ZERO_MODE -- Performing Test HAVE_FLUSH_ZERO_MODE - Success -- Performing Test HAVE_DENORMALS_ZERO_MODE -- Performing Test HAVE_DENORMALS_ZERO_MODE - Failed -- Looking for erfc -- Looking for erfc - not found -- Looking for getpid -- Looking for getpid - found -- Looking for _mm_malloc -- Looking for _mm_malloc - not found -- Looking for popen -- Looking for popen - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strsep -- Looking for strsep - found -- Looking for sysctl -- Looking for sysctl - not found -- Looking for times -- Looking for times - found -- Looking for fstat -- Looking for fstat - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for stat -- Looking for stat - found CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/Blaze_Import.cmake:51 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Call Stack (most recent call first): /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/CMakeLists.txt:7 (Blaze_Import) -- Configuring blaze version 3.8 -- Configured C++11 for multithreading. -- Configuring Vectorization : ON -- Automatic Cache Size Configuration -- Configuring Cache Size : 4194304UL -- Blaze has been configured successfully -- Enabling BayesHammer as a dependency to SPAdes -- Enabling IonHammer as a dependency to SPAdes -- Enabling Corrector as a dependency to SPAdes -- spades project is enabled -- hammer project is enabled -- ionhammer project is enabled -- corrector project is enabled -- spaligner project is disabled -- spades_tools project is enabled -- binspreader project is disabled -- pathracer project is disabled -- mts project is disabled -- online_vis project is disabled -- cds_subgraphs project is disabled -- Configuring done (16.6s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_build -- all debruijn_test include_test cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 0%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o [ 0%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o [ 0%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o [ 1%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o [ 1%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o [ 1%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o [ 1%] Building CXX object ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o [ 2%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o [ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib/edlib.cpp [ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o [ 2%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o [ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o [ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o [ 3%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest/teamcity_gtest.cpp [ 4%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o [ 4%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o [ 4%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o [ 6%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -MF CMakeFiles/gqf.dir/gqf.c.o.d -o CMakeFiles/gqf.dir/gqf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c [ 6%] Building CXX object common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -pedantic-errors -Werror -Wall -Wextra -Wconversion -Wsign-conversion -Wno-parentheses -Wno-unused-local-typedefs -Wno-array-bounds -Wno-maybe-uninitialized -Wno-restrict -MD -MT ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o -MF CMakeFiles/lexy_file.dir/input/file.cpp.o.d -o CMakeFiles/lexy_file.dir/input/file.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/input/file.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat/format.cc cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o -MF CMakeFiles/zlibstatic.dir/adler32.c.o.d -o CMakeFiles/zlibstatic.dir/adler32.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/adler32.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -MF CMakeFiles/llvm-support.dir/APFloat.cpp.o.d -o CMakeFiles/llvm-support.dir/APFloat.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/APFloat.cpp [ 6%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/genomic_info.cpp [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/APInt.cpp [ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alloc.c.o [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -fPIC -Wno-deprecated -O2 -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -ftls-model=initial-exec -fno-builtin-malloc -MD -MT ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -MF CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/src/static.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest/teamcity_messages.cpp [ 7%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Atomic.cpp [ 7%] Building C object ext/easel/CMakeFiles/easel.dir/esl_arr2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -MF CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp [ 7%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/version.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -MF CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o.d -o CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o -MF CMakeFiles/zlibstatic.dir/adler32_fold.c.o.d -o 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o -MF CMakeFiles/zlibstatic.dir/chunkset.c.o.d -o CMakeFiles/zlibstatic.dir/chunkset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/chunkset.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Debug.cpp cd 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CMakeFiles/easel.dir/easel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o -MF CMakeFiles/zlibstatic.dir/compare256.c.o.d -o CMakeFiles/zlibstatic.dir/compare256.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compare256.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o [ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Errno.cpp [ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o [ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Error.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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-I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o -MF CMakeFiles/easel.dir/esl_arr3.c.o.d -o CMakeFiles/easel.dir/esl_arr3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_arr3.c cd 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CMakeFiles/easel.dir/esl_cluster.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cluster.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Hashing.cpp [ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o [ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o [ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_buffer.c [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o -MF CMakeFiles/zlibstatic.dir/compress.c.o.d -o CMakeFiles/zlibstatic.dir/compress.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compress.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o -MF CMakeFiles/easel.dir/esl_bitfield.c.o.d -o CMakeFiles/easel.dir/esl_bitfield.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_bitfield.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o -MF CMakeFiles/zlibstatic.dir/cpu_features.c.o.d -o CMakeFiles/zlibstatic.dir/cpu_features.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/cpu_features.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/FormatVariadic.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o -MF CMakeFiles/zlibstatic.dir/crc32_braid.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_braid.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_braid.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/CrashRecoveryContext.cpp [ 8%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -MF CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_braid_comb.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o -MF CMakeFiles/zlibstatic.dir/crc32_fold.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_fold.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_fold.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/FoldingSet.cpp [ 9%] Linking CXX static library libversion.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o -MF CMakeFiles/zlibstatic.dir/deflate.c.o.d -o CMakeFiles/zlibstatic.dir/deflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:612:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 612 | printf("%02llx ", j); | ~~~~~^ ~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_dump': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 644 | qf->metadata->nblocks, | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 644 | qf->metadata->nblocks, 645 | qf->metadata->ndistinct_elts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu ...... 646 | qf->metadata->nelts); | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_deserialize': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:1609:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1609 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o -MF CMakeFiles/zlibstatic.dir/deflate_fast.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_fast.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_fast.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:1618:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1618 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o -MF CMakeFiles/zlibstatic.dir/deflate_huff.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_huff.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_huff.c [ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o -MF CMakeFiles/zlibstatic.dir/deflate_medium.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_medium.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_medium.c [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/JSON.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LEB128.cpp [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Host.cpp [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o [ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o -MF CMakeFiles/zlibstatic.dir/deflate_quick.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_quick.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_quick.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LineIterator.cpp [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o -MF CMakeFiles/easel.dir/esl_cpu.c.o.d -o CMakeFiles/easel.dir/esl_cpu.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cpu.c [ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o -MF CMakeFiles/zlibstatic.dir/deflate_rle.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_rle.c /usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o /usr/bin/ranlib libversion.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 12%] Built target version [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dirichlet.c [ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o -MF CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_slow.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_slow.c [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MD5.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Locale.cpp [ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o -MF CMakeFiles/zlibstatic.dir/deflate_stored.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_stored.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_stored.c [ 13%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o -MF CMakeFiles/zlibstatic.dir/functable.c.o.d -o CMakeFiles/zlibstatic.dir/functable.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/functable.c [ 13%] Linking CXX static library liblexy_file.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -P CMakeFiles/lexy_file.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lexy_file.dir/link.txt --verbose=1 [ 13%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o -MF CMakeFiles/zlibstatic.dir/infback.c.o.d -o CMakeFiles/zlibstatic.dir/infback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/infback.c [ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ManagedStatic.cpp [ 14%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MemAlloc.cpp [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_distance.c /usr/bin/ar qc liblexy_file.a CMakeFiles/lexy_file.dir/input/file.cpp.o /usr/bin/ranlib liblexy_file.a [ 15%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MemoryBuffer.cpp [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dsqdata.c [ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o [ 15%] Built target lexy_file cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o -MF CMakeFiles/zlibstatic.dir/inflate.c.o.d -o CMakeFiles/zlibstatic.dir/inflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/inflate.c [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dmatrix.c [ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o -MF CMakeFiles/zlibstatic.dir/inftrees.c.o.d -o CMakeFiles/zlibstatic.dir/inftrees.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/inftrees.c [ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o -MF CMakeFiles/zlibstatic.dir/insert_string.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string.c [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_exponential.c [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_fileparser.c [ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o -MF CMakeFiles/zlibstatic.dir/insert_string_roll.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string_roll.c [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gamma.c [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gencode.c [ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/NativeFormatting.cpp [ 18%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o -MF CMakeFiles/zlibstatic.dir/slide_hash.c.o.d -o CMakeFiles/zlibstatic.dir/slide_hash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/slide_hash.c [ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Path.cpp [ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp [ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Program.cpp [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Regex.cpp [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.c.o -MF CMakeFiles/zlibstatic.dir/trees.c.o.d -o CMakeFiles/zlibstatic.dir/trees.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/trees.c [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Signals.cpp [ 19%] Linking CXX static library libmph_index.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -P CMakeFiles/mph_index.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -E cmake_link_script CMakeFiles/mph_index.dir/link.txt --verbose=1 [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SmallVector.cpp [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SourceMgr.cpp [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o -MF CMakeFiles/zlibstatic.dir/uncompr.c.o.d -o CMakeFiles/zlibstatic.dir/uncompr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/uncompr.c /usr/bin/ar qc libmph_index.a CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o /usr/bin/ranlib libmph_index.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 19%] Built target mph_index [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringExtras.cpp [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.c.o -MF CMakeFiles/zlibstatic.dir/zutil.c.o.d -o CMakeFiles/zlibstatic.dir/zutil.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/zutil.c [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mxsave -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o -c 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ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringMap.cpp [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringRef.cpp [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringSaver.cpp [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_getopts.c [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_avx2.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ThreadLocal.cpp [ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_avx2.c [ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_avx2.c [ 21%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Threading.cpp [ 21%] Linking C static library libgqf.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 [ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gev.c [ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx2.c [ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o [ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_graph.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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/usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 21%] Built target gqf [ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512_vnni.c [ 21%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/TimeProfiler.cpp [ 21%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Twine.cpp [ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gumbel.c [ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_heap.c [ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o [ 23%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Unicode.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_sse42.c [ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/insert_string_sse42.c [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/WithColor.cpp [ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o [ 25%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o [ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o [ 25%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_histogram.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_sse2.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLParser.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_sse2.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp:100: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] 94 | mi = ::mallinfo(); | ~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:35: /usr/include/malloc.h:114:24: note: declared here 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; | ^~~~~~~~ [ 25%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_sse2.c [ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLTraits.cpp [ 26%] Linking CXX static library libteamcity_gtest.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 [ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_os_ostream.cpp [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hmm.c [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o -MF CMakeFiles/easel.dir/esl_huffman.c.o.d -o CMakeFiles/easel.dir/esl_huffman.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_huffman.c [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o [ 28%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hyperexp.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_ostream.cpp [ 28%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_ssse3.c [ 28%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o [ 28%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regcomp.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_ssse3.c [ 28%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regerror.c [ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_iset.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_iset.c.o -MF CMakeFiles/easel.dir/esl_iset.c.o.d -o CMakeFiles/easel.dir/esl_iset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_iset.c [ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_json.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_json.c.o -MF CMakeFiles/easel.dir/esl_json.c.o.d -o CMakeFiles/easel.dir/esl_json.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_json.c [ 28%] Linking CXX static library libedlib.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 /usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o /usr/bin/ranlib libteamcity_gtest.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 28%] Built target teamcity_gtest [ 29%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o [ 29%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o [ 29%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_pclmulqdq.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regexec.c [ 29%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_vpclmulqdq.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regfree.c [ 29%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regstrlcpy.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_keyhash.c [ 30%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o -MF CMakeFiles/zlibstatic.dir/gzlib.c.o.d -o CMakeFiles/zlibstatic.dir/gzlib.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzlib.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o -MF CMakeFiles/easel.dir/esl_lognormal.c.o.d -o CMakeFiles/easel.dir/esl_lognormal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_lognormal.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o -MF CMakeFiles/easel.dir/esl_matrixops.c.o.d -o CMakeFiles/easel.dir/esl_matrixops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_matrixops.c [ 30%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o -MF CMakeFiles/zlibstatic.dir/gzread.c.o.d -o CMakeFiles/zlibstatic.dir/gzread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/gzread.c [ 30%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o -MF CMakeFiles/zlibstatic.dir/gzwrite.c.o.d -o CMakeFiles/zlibstatic.dir/gzwrite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzwrite.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mem.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_minimizer.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixgev.c [ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msa.c [ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -MF CMakeFiles/easel.dir/esl_msacluster.c.o.d -o CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msacluster.c [ 31%] Built target edlib make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong 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/build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile2.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_a2m.c make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp:326:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] 326 | if (converged_ && Valley_ > x[2] && x[2] > 2) { | ^~~~~~~ [ 32%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/sequence_tools.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp:360:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 360 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? | ^~~~~~~ [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_afa.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_clustal.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_phylip.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_stockholm.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_selex.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msashuffle.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msaweight.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_normal.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_paml.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_random.c [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_quicksort.c.o /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:364:10: warning: unused variable 'loaded' [-Wunused-variable] 364 | bool loaded = base::BinRead(is, gp); | ^~~~~~ cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_quicksort.c.o -MF CMakeFiles/easel.dir/esl_quicksort.c.o.d -o CMakeFiles/easel.dir/esl_quicksort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_quicksort.c [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o -MF CMakeFiles/easel.dir/esl_rand64.c.o.d -o CMakeFiles/easel.dir/esl_rand64.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rand64.c [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_randomseq.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ratematrix.c [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_recorder.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o -MF CMakeFiles/easel.dir/esl_red_black.c.o.d -o CMakeFiles/easel.dir/esl_red_black.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_red_black.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_regexp.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rootfinder.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sq.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio.c [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ascii.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:208:19: required from here 208 | graph_io_.Load(basename, g); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:211:45: required from here 211 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:214:34: required from here 214 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:217:35: required from here 217 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:220:41: required from here 220 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:254:22: required from here 254 | graph_io_.BinRead(is, gp.get_mutable()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:257:45: required from here 257 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:260:34: required from here 260 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:263:35: required from here 263 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:266:41: required from here 266 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ncbi.c [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ssi.c [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stack.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stats.c [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stopwatch.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stretchexp.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o -MF CMakeFiles/easel.dir/esl_subcmd.c.o.d -o CMakeFiles/easel.dir/esl_subcmd.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_subcmd.c [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_threads.c [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o [ 40%] Linking C static library libz.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_tree.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cmake -P CMakeFiles/zlibstatic.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/zlibstatic.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:22: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:179:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 179 | if ( ((p) = malloc(size)) == NULL) { \ | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:71:3: note: in expansion of macro 'ESL_ALLOC' 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:21: /usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ [ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_varint.c.o [ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_varint.c.o -MF CMakeFiles/easel.dir/esl_varint.c.o.d -o CMakeFiles/easel.dir/esl_varint.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_varint.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_vectorops.c [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_weibull.c [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_workqueue.c [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_wuss.c [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sse.c [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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-DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o -MF CMakeFiles/easel.dir/esl_avx512.c.o.d -o CMakeFiles/easel.dir/esl_avx512.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_avx512.c [ 42%] Building C object ext/easel/CMakeFiles/easel.dir/esl_neon.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT 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CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o CMakeFiles/zlibstatic.dir/gzlib.c.o CMakeFiles/zlibstatic.dir/gzread.c.o CMakeFiles/zlibstatic.dir/gzwrite.c.o /usr/bin/ranlib libz.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 42%] Built target zlibstatic make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E 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Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 42%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_import.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection 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-Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kstring.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c [ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwt.c.o [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwt.c.o -MF CMakeFiles/bwa.dir/bwt.c.o.d -o CMakeFiles/bwa.dir/bwt.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_pileup.c [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_md.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_lpileup.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o -MF CMakeFiles/samtools.dir/bgzf.c.o.d -o CMakeFiles/samtools.dir/bgzf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bgzf.c [ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o [ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o -MF CMakeFiles/bwa.dir/bntseq.c.o.d -o CMakeFiles/bwa.dir/bntseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bntseq.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwa.c.o -MF CMakeFiles/bwa.dir/bwa.c.o.d -o CMakeFiles/bwa.dir/bwa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwa.c [ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o -MF CMakeFiles/bwa.dir/bwamem_pair.c.o.d -o CMakeFiles/bwa.dir/bwamem_pair.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_pair.c [ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o -MF CMakeFiles/bwa.dir/bwamem.c.o.d -o CMakeFiles/bwa.dir/bwamem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem.c [ 47%] Linking CXX static library libformat.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o -MF CMakeFiles/bwa.dir/bwamem_extra.c.o.d -o CMakeFiles/bwa.dir/bwamem_extra.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_extra.c [ 48%] Building C object ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o -MF CMakeFiles/bwa.dir/malloc_wrap.c.o.d -o CMakeFiles/bwa.dir/malloc_wrap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/malloc_wrap.c [ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c [ 48%] Building C object ext/bwa/CMakeFiles/bwa.dir/is.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/is.c.o -MF CMakeFiles/bwa.dir/is.c.o.d -o CMakeFiles/bwa.dir/is.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/is.c [ 48%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o -MF CMakeFiles/bwa.dir/bwtindex.c.o.d -o CMakeFiles/bwa.dir/bwtindex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtindex.c [ 48%] Building C object ext/bwa/CMakeFiles/bwa.dir/rope.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rope.c.o -MF CMakeFiles/bwa.dir/rope.c.o.d -o CMakeFiles/bwa.dir/rope.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_flush': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function '_razf_write': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_close': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'save_zindex': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o /usr/bin/ranlib libformat.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore_node': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/faidx.c [ 48%] Built target format [ 48%] Building C object ext/bwa/CMakeFiles/bwa.dir/rle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rle.c.o -MF CMakeFiles/bwa.dir/rle.c.o.d -o CMakeFiles/bwa.dir/rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rle.c [ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o [ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o [ 50%] Building C object ext/bwa/CMakeFiles/bwa.dir/kstring.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bedidx.c [ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/kstring.c.o -MF CMakeFiles/bwa.dir/kstring.c.o.d -o CMakeFiles/bwa.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kstring.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/sam_header.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_sort.c [ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_reheader.c [ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o [ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o [ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o -MF CMakeFiles/samtools.dir/knetfile.c.o.d -o CMakeFiles/samtools.dir/knetfile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_cat.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kprobaln.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:46: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'khttp_connect_file': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:69:77: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 69 | auto exponent = exp_char >> (dsl::lit_c<'+'> | dsl::lit_c<'-'>) + dsl::digits<>; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:74:40: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 71 | dsl::position + | ~~~~~~~~~~~~~~~ 72 | integer + | ~~~~~~~~~ 73 | dsl::if_(fraction) + | ~~~~~~~~~~~~~~~~~~~~ 74 | dsl::if_(exponent) + | ~~~~~~~~~~~~~~~~~~~^ 75 | dsl::position; | ~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:94:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 94 | dsl::capture(LEXY_LIT("A")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:95:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 95 | dsl::capture(LEXY_LIT("i")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:96:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 96 | dsl::capture(LEXY_LIT("f")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:97:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 97 | dsl::capture(LEXY_LIT("Z")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:98:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 98 | dsl::capture(LEXY_LIT("J")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:99:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 99 | dsl::capture(LEXY_LIT("H")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:100:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 100 | dsl::capture(LEXY_LIT("B")) >> colon + dsl::p | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:162:40: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 162 | return dsl::eof | (tab >> tags + dsl::eof); | ~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: At global scope: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:191:56: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 189 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 | tab + (LEXY_LIT("*") | | ~~~~~~~~~~~~~~~~~~~~~~ 191 | dsl::identifier(dsl::ascii::alpha)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 192 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:216:58: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 212 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | tab + (LEXY_LIT("*") | dsl::p) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 217 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:246:54: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 244 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~ 246 | tab + (LEXY_LIT("*") | dsl::p) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 247 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:269:41: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 269 | dsl::ascii::alpha >> tab + dsl::until(dsl::newline).or_eof() | | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Linking CXX static library libsequence.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 [ 51%] Linking C static library libeasel.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In instantiation of 'gfa::grammar::cigar_string::cigarop:: [with auto:48 = lexy::lexeme; uint32_t = unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/callback/base.hpp:19:60: required by substitution of 'template using lexy::_detect_callback_for = decltype (declval()((declval)()...)) [with T = lexy::_callback >; Args = {unsigned int&, lexy::lexeme&&}]' 19 | using _detect_callback_for = decltype(LEXY_DECLVAL(const T)(LEXY_DECLVAL(Args)...)); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/_detail/detect.hpp:28:60: required from 'constexpr const bool lexy::_detail::is_detected using lexy::_detect_callback_for = decltype (declval()((declval)()...)), lexy::_callback >, unsigned int&, lexy::lexeme&&>' 28 | constexpr bool is_detected = _detector::value; | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/callback/base.hpp:22:16: required from 'constexpr const bool lexy::is_callback_for >, unsigned int&, lexy::lexeme&&>' 22 | = _detail::is_detected<_detect_callback_for, std::decay_t, Args...>; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/grammar.hpp:353:34: required from 'constexpr lexy::production_value_callback::return_type lexy::production_value_callback::operator()(Args&& ...) const [with Args = {unsigned int&, lexy::lexeme}; Production = gfa::grammar::cigar_string::cigarop; ParseState = void; return_type = gfa::cigarop]' 353 | else if constexpr (lexy::is_callback_for<_type, Args&&...>) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/_detail/lazy_init.hpp:130:36: [ skipping 30 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/dsl/choice.hpp:108:60: required from 'lexyd::_chc, lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_br, lexyd::_until_eof >, lexyd::_br, lexyd::_until_eof >, lexyd::_err >::p::parse, void, gfa::grammar::record, void>, lexy::_prd>(lexy::_pc, void, gfa::grammar::record, void>&, lexy::_prd&):: [with auto:42 = lexyd::_prd::bp]' 108 | result = parser.template finish(context, reader, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 109 | static_cast(args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/dsl/choice.hpp:114:39: required from 'static constexpr bool lexyd::_chc::p::parse(Context&, Reader&, Args&& ...) [with Context = lexy::_pc, void, gfa::grammar::record, void>; Reader = lexy::_prd; Args = {}; NextParser = lexy::_detail::final_parser; R = {lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_br, lexyd::_until_eof >, lexyd::_br, lexyd::_until_eof >, lexyd::_err}]' 114 | auto found_branch = (try_r(lexy::branch_parser_for{}) || ...); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/base.hpp:210:37: required from 'constexpr auto lexy::_do_action(_pc&, Reader&) [with Handler = _ph<_prd>; State = void; Production = gfa::grammar::record; Reader = _prd; typename std::conditional<_production_defines_whitespace, Production, void>::type = void]' 210 | auto rule_result = parser::parse(context, reader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/base.hpp:236:34: required from 'constexpr auto lexy::do_action(Handler&&, State*, Reader&) [with Production = gfa::grammar::record; Result = parse_action, lexy_ext::_report_error >::result_type; Handler = _ph<_prd>; State = void; Reader = _prd]' 236 | auto rule_result = _do_action(context, reader); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/parse.hpp:164:56: required from 'constexpr auto lexy::parse_action::operator()(Production, const Input&) const [with Production = gfa::grammar::record; State = void; Input = lexy::string_input; ErrorCallback = lexy_ext::_report_error]' 164 | return lexy::do_action(handler(input_holder, sink), _state, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 | reader); | ~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/parse.hpp:173:62: required from 'constexpr auto lexy::parse(const Input&, const ErrorCallback&) [with Production = gfa::grammar::record; Input = string_input; ErrorCallback = lexy_ext::_report_error]' 173 | return parse_action(callback)(Production{}, input); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:280:47: required from here 280 | auto result = lexy::parse(lexy::string_input(line, len), lexy_ext::report_error); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:151:37: warning: conversion from 'uint32_t' {aka 'unsigned int'} to 'unsigned int:24' may change value [-Wconversion] 151 | return gfa::cigarop{cnt, lexeme[0]}; | ^~~ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 51%] Built target mimalloc-obj make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o /usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 51%] Built target sequence make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o [ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o [ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o [ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o [ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o [ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o [ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger_impl.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/memory_limit.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/temporary.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/glob.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o -MF CMakeFiles/utils.dir/logger/log_writers.cpp.o.d -o CMakeFiles/utils.dir/logger/log_writers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/log_writers.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdutils.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g 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static library libsamtools.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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-O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/seqmodel.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_alidisplay.c /usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/bgzf.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmm.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmm.c.o -c 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -MF CMakeFiles/hmmer.dir/src/p7_null3.c.o.d -o CMakeFiles/hmmer.dir/src/p7_null3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_null3.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_pipeline.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_prior.c [ 62%] Built target samtools make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_profile.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_spensemble.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_tophits.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_trace.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_scoredata.c [ 62%] Building CXX object common/io/sam/CMakeFiles/samio.dir/read.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/read.cpp.o -MF CMakeFiles/samio.dir/read.cpp.o.d -o CMakeFiles/samio.dir/read.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/read.cpp [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o -MF CMakeFiles/hmmer.dir/src/p7_hit.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hit.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hit.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -MF CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o.d -o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmpgmd2msa.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o -MF CMakeFiles/hmmer.dir/src/p7_domain.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domain.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_domain.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -MF CMakeFiles/hmmer.dir/src/fm_alphabet.c.o.d -o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_alphabet.c [ 63%] Building CXX object common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o -MF CMakeFiles/samio.dir/sam_reader.cpp.o.d -o CMakeFiles/samio.dir/sam_reader.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/sam_reader.cpp [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -MF CMakeFiles/hmmer.dir/src/fm_general.c.o.d -o CMakeFiles/hmmer.dir/src/fm_general.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_general.c [ 63%] Building CXX object common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o -MF CMakeFiles/samio.dir/bam_parser.cpp.o.d -o CMakeFiles/samio.dir/bam_parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/bam_parser.cpp [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_sse.c [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_ssv.c [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/fwdback.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/ssvfilter.c [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/msvfilter.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/optacc.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/vitfilter.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/mpi.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:108:13: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' 108 | DeleteLink(graph_.conjugate(w), graph_.conjugate(in_edge)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp:185:25: required from here 185 | helper.LinkEdges(e1, e2); | ~~~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ [ 68%] Linking CXX static library libllvm-support.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake [ 69%] Linking C static library libbwa.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -P CMakeFiles/bwa.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -E cmake_link_script CMakeFiles/bwa.dir/link.txt --verbose=1 [ 69%] Linking CXX static library libcoverage_model.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 /usr/bin/ar qc libbwa.a CMakeFiles/bwa.dir/utils.c.o CMakeFiles/bwa.dir/kthread.c.o CMakeFiles/bwa.dir/ksw.c.o CMakeFiles/bwa.dir/bwt.c.o CMakeFiles/bwa.dir/bntseq.c.o CMakeFiles/bwa.dir/bwa.c.o CMakeFiles/bwa.dir/bwamem.c.o CMakeFiles/bwa.dir/bwamem_pair.c.o CMakeFiles/bwa.dir/bwamem_extra.c.o CMakeFiles/bwa.dir/malloc_wrap.c.o CMakeFiles/bwa.dir/is.c.o CMakeFiles/bwa.dir/bwtindex.c.o CMakeFiles/bwa.dir/rope.c.o CMakeFiles/bwa.dir/rle.c.o CMakeFiles/bwa.dir/kstring.c.o /usr/bin/ranlib libbwa.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 69%] Built target bwa make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/spades-bwa.dir/DependInfo.cmake "--color=" /usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o /usr/bin/ranlib libcoverage_model.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/build [ 69%] Built target coverage_model make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o [ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bamlite.c.o [ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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Building C object ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o -MF CMakeFiles/spades-bwa.dir/bwtaln.c.o.d -o CMakeFiles/spades-bwa.dir/bwtaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtaln.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/pemerge.c.o -MF CMakeFiles/spades-bwa.dir/pemerge.c.o.d -o CMakeFiles/spades-bwa.dir/pemerge.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/pemerge.c [ 70%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.c.o -MF CMakeFiles/spades-bwa.dir/fastmap.c.o.d -o CMakeFiles/spades-bwa.dir/fastmap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/fastmap.c [ 70%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o -MF CMakeFiles/spades-bwa.dir/maxk.c.o.d -o CMakeFiles/spades-bwa.dir/maxk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/maxk.c [ 70%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o -MF CMakeFiles/spades-bwa.dir/bwtgap.c.o.d -o CMakeFiles/spades-bwa.dir/bwtgap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtgap.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o -MF CMakeFiles/spades-bwa.dir/kopen.c.o.d -o CMakeFiles/spades-bwa.dir/kopen.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c [ 71%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o [ 71%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o [ 71%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o -MF CMakeFiles/spades-bwa.dir/bwaseqio.c.o.d -o CMakeFiles/spades-bwa.dir/bwaseqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwaseqio.c [ 71%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o [ 71%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o [ 73%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_main.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o -MF CMakeFiles/spades-bwa.dir/bwashm.c.o.d -o CMakeFiles/spades-bwa.dir/bwashm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c [ 73%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_aux.c [ 73%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwase.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_core.c [ 73%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_chain.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o -MF CMakeFiles/spades-bwa.dir/bwt_lite.c.o.d -o CMakeFiles/spades-bwa.dir/bwt_lite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt_lite.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o -MF CMakeFiles/spades-bwa.dir/bwape.c.o.d -o CMakeFiles/spades-bwa.dir/bwape.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwape.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwase.c.o -MF CMakeFiles/spades-bwa.dir/bwase.c.o.d -o CMakeFiles/spades-bwa.dir/bwase.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwase.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_pair.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c: In function 'bwa_shm_stage': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:29:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:66:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:548, from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:6: In function 'strncpy', inlined from 'cmd2argv' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:246:2, inlined from 'kopen' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:307:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' specified bound between 18446744071562067969 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'cmd2argv', inlined from 'kopen' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:307:13: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:245:32: warning: argument 1 range [18446744071562067970, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 245 | argv[0] = str = (char*)calloc(end - beg + 1, 1); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:7: /usr/include/stdlib.h: In function 'kopen': /usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" /usr/bin/ranlib libllvm-support.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 73%] Built target llvm-support [ 73%] Linking CXX static library libsamio.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/cmake -P CMakeFiles/samio.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/cmake -E cmake_link_script CMakeFiles/samio.dir/link.txt --verbose=1 [ 73%] Linking CXX static library libutils.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libsamio.a CMakeFiles/samio.dir/read.cpp.o CMakeFiles/samio.dir/sam_reader.cpp.o CMakeFiles/samio.dir/bam_parser.cpp.o /usr/bin/ranlib libsamio.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 73%] Built target samio /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o CMakeFiles/utils.dir/logger/log_writers.cpp.o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 73%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/id_distributor.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/components/connected_component.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.cpp [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp [ 74%] Linking C executable ../../bin/spades-bwa cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-bwa.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-bwa.dir/link.d "CMakeFiles/spades-bwa.dir/main.c.o" "CMakeFiles/spades-bwa.dir/fastmap.c.o" "CMakeFiles/spades-bwa.dir/pemerge.c.o" "CMakeFiles/spades-bwa.dir/maxk.c.o" "CMakeFiles/spades-bwa.dir/kopen.c.o" "CMakeFiles/spades-bwa.dir/bwtaln.c.o" "CMakeFiles/spades-bwa.dir/bwtgap.c.o" "CMakeFiles/spades-bwa.dir/bwaseqio.c.o" "CMakeFiles/spades-bwa.dir/bamlite.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o" "CMakeFiles/spades-bwa.dir/bwashm.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o" "CMakeFiles/spades-bwa.dir/bwt_lite.c.o" "CMakeFiles/spades-bwa.dir/bwape.c.o" "CMakeFiles/spades-bwa.dir/bwase.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o" -o ../../bin/spades-bwa libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Built target spades-bwa [ 74%] Linking CXX static library libgraphio.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa.cpp.o CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o /usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Built target graphio [ 74%] Linking C static library libhmmer.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/p7_hit.c.o CMakeFiles/hmmer.dir/src/p7_domain.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o /usr/bin/ranlib libhmmer.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Built target hmmer make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o [ 74%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_info_updater.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_index_builders.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': /usr/include/c++/14/bits/stl_vector.h:1018:43: required from 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; size_type = long unsigned int]' 1018 | _M_erase_at_end(this->_M_impl._M_start + __new_size); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map.hpp:166:21: required from 'void kmers::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = kmers::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' 166 | data_.resize(sz); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp:31:21: required from 'kmers::KMerDiskStorage kmers::PerfectHashMapBuilder::BuildIndex(kmers::PerfectHashMap&, Counter&, size_t, size_t, bool) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = kmers::InvertableStoring; Counter = kmers::KMerDiskCounter >; typename Counter::Seq = RuntimeSeq<128>; size_t = long unsigned int]' 31 | index.resize(res.total_kmers()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp:140:39: required from 'void kmers::BuildIndex(PerfectHashMap&, Counter&, size_t, size_t, bool) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmer_index_traits >; StoringType = InvertableStoring; Counter = KMerDiskCounter >; size_t = long unsigned int]' 140 | PerfectHashMapBuilder().BuildIndex(index, counter, bucket_num, thread_num, save_final); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_index_builders.hpp:280:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&, fs::impl::TmpDir, size_t) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' 280 | BuildIndex(index, counter, 10 * nthreads, nthreads); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:29:43: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&, bool) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' 29 | IndexBuilder().BuildIndexFromGraph(index, g, fs::tmp::make_temp_dir(workdir_, "edge_index")); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:36:70: required from here 36 | void EdgeIndexRefiller::Refill(EdgeIndex &index, const Graph &g, bool); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_position_index.hpp:21:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 21 | IdHolder edge_id_; | ^~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp: In constructor 'hmmer::HMMFile::HMMFile(const std::string&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:53:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:55:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:57:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 57 | p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp:166:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 166 | pli->Z = pli->domZ = cfg.Z; | ~~~~^ [ 74%] Linking CXX static library libhmmercpp.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o /usr/bin/ranlib libhmmercpp.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Built target hmmercpp make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o [ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o [ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o [ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o [ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/distance_estimation.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/mismatch_correction.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pair_info_count.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/contig_output_stage.cpp [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/chromosome_removal.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/extract_domains.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/restricted_edges_filling.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/load_graph.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -MF CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o.d -o CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/wastewater_disentangle.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(graph_pack::GraphPack&, const char*)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp:26:9: warning: unused variable 'code' [-Wunused-variable] 26 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp:53:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 53 | if (seqpos2.second - seqpos2.first < model_length / 10) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 329 | while (pref_remove < coverages.size() && coverages[pref_remove] < cov / 2 ) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:485:14: warning: unused variable 'u1' [-Wunused-variable] 485 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:486:14: warning: unused variable 'u2' [-Wunused-variable] 486 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] 659 | size_t cur_len = end_it - start_it; | ^~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/stacktrace.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/verify.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/binary.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/io_base.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:10: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:12: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp:232:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 232 | for (;index != res.first; ++index) { | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp:259:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 259 | if (coords.second + 5000 > path.Length()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:536:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper_notifier.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:434:46: required from here 434 | omnigraph::CompressAllVertices(g_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:752:28: required from here 752 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:17: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 78%] Linking CXX static library libbinary_io.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 /usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o /usr/bin/ranlib libbinary_io.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Built target binary_io make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain/CMakeFiles/toolchain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/build make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 79%] Building CXX object common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o [ 79%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/paired_readers.cpp [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o -MF CMakeFiles/toolchain.dir/utils.cpp.o.d -o CMakeFiles/toolchain.dir/utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/parser.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_converter.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/read_converter.cpp [ 79%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_streams.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/io_helper.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/dataset_readers.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:62:63: required from here 62 | io::binary::BasicGraphIO().Load(filename, graph); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 79%] Linking CXX static library libassembly_graph.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 /usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 79%] Built target assembly_graph make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 79%] Building CXX object common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o -MF CMakeFiles/alignment.dir/long_read_mapper.cpp.o.d -o CMakeFiles/alignment.dir/long_read_mapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp [ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o -MF CMakeFiles/alignment.dir/gap_info.cpp.o.d -o CMakeFiles/alignment.dir/gap_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/gap_info.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o -MF CMakeFiles/alignment.dir/bwa_index.cpp.o.d -o CMakeFiles/alignment.dir/bwa_index.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o -MF CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o.d -o CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_sequence_mapper.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o -MF CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper_notifier.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -MF CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_dijkstra.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o -MF CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/g_aligner.cpp [ 80%] Linking CXX static library libtoolchain.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -P CMakeFiles/toolchain.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -E cmake_link_script CMakeFiles/toolchain.dir/link.txt --verbose=1 /usr/bin/ar qc libtoolchain.a CMakeFiles/toolchain.dir/utils.cpp.o /usr/bin/ranlib libtoolchain.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 80%] Built target toolchain [ 81%] Linking CXX static library libinput.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Built target input make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Building CXX object common/library/CMakeFiles/library.dir/library_data.cpp.o [ 81%] Building CXX object common/library/CMakeFiles/library.dir/library.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library_data.cpp.o -MF CMakeFiles/library.dir/library_data.cpp.o.d -o CMakeFiles/library.dir/library_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library_data.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library.cpp.o -MF CMakeFiles/library.dir/library.cpp.o.d -o CMakeFiles/library.dir/library.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp: In member function 'omnigraph::MappingPath alignment::BWAIndex::GetMappingPath(const mem_alnreg_v&, const Sequence&, bool) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:335:29: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'long unsigned int' [-Wformat=] 335 | fprintf(stderr, "%zu: [%zu, %lld)\t[%d, %d) %c %ld %s %d %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | i, 337 | pos, pos + a.re - a.rb, a.qb, a.qe, | ~~~~~~~~~~~~~~~~~ | | | long unsigned int /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:152:13: note: in definition of macro 'LOG_EXPR' 152 | expr; \ | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:331:9: note: in expansion of macro 'DEBUG_EXPR' 331 | DEBUG_EXPR({ | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:335:44: note: format string is defined here 335 | fprintf(stderr, "%zu: [%zu, %lld)\t[%d, %d) %c %ld %s %d %d\n", | ~~~^ | | | long long int | %ld In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'Sequence debruijn_graph::MergeSequences(const Graph&, const std::vector&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp:18:41: required from here 18 | Sequence merged_seq = MergeSequences(g_, path); | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp:120:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 120 | auto end = g.EdgeEnd(continuous_path[i - 1]); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp:280:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 280 | if (bad_mapping_pos == -1) | ~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_dijkstra.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:9: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 81%] Linking CXX static library liblibrary.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/cmake -P CMakeFiles/library.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/cmake -E cmake_link_script CMakeFiles/library.dir/link.txt --verbose=1 /usr/bin/ar qc liblibrary.a CMakeFiles/library.dir/library.cpp.o CMakeFiles/library.dir/library_data.cpp.o /usr/bin/ranlib liblibrary.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/configs/CMakeFiles/configs.dir/config_struct.cpp.o [ 82%] Building CXX object common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o -MF CMakeFiles/configs.dir/pe_config_struct.cpp.o.d -o CMakeFiles/configs.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/pe_config_struct.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/config_struct.cpp.o -MF CMakeFiles/configs.dir/config_struct.cpp.o.d -o CMakeFiles/configs.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/config_struct.cpp In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:9: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:13: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 82%] Linking CXX static library libalignment.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/gap_info.cpp.o CMakeFiles/alignment.dir/bwa_index.cpp.o CMakeFiles/alignment.dir/long_read_mapper.cpp.o CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 82%] Built target alignment make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o [ 84%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o [ 84%] Building CXX object common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/genome_consistance_checker.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -MF CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d -o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaff_supplementary.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.hpp:8, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:6: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:40:58: required from here 40 | for (auto it = g.SmartVertexBegin(); ! it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:137:64: required from here 137 | for (auto iter = graph.SmartEdgeBegin(); ! iter.IsEnd(); ++iter) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:21: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::const_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:633:18: required from here 633 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:674:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] 674 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/stacktrace.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/verify.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/binary.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_storage.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.hpp:11: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 84%] Linking CXX static library libconfigs.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -P CMakeFiles/configs.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -E cmake_link_script CMakeFiles/configs.dir/link.txt --verbose=1 /usr/bin/ar qc libconfigs.a CMakeFiles/configs.dir/config_struct.cpp.o CMakeFiles/configs.dir/pe_config_struct.cpp.o /usr/bin/ranlib libconfigs.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 84%] Built target configs make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_detector.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_traverser.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/overlap_remover.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pe_resolver.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/gap_analyzer.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o [ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launch_support.cpp [ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o [ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launcher.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/extenders_logic.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:118:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 118 | if (iter->second < min_read_count_) { | ^~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:36:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 36 | if (sum < absolute_weight_threshold_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp: In member function 'bool path_extend::LoopDetectingPathExtender::TryToResolveHairpin(path_extend::BidirectionalPath&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp:124:12: warning: variable 'pin' set but not used [-Wunused-but-set-variable] 124 | EdgeId pin = path[path.Size() - 2]; | ^~~ [ 86%] Linking CXX static library libspades-stages.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_visualizer.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launcher.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" "CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o" /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target spades-stages [ 86%] Linking CXX static library libmodules.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/weighted_distance_estimation.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -MF CMakeFiles/paired_info.dir/paired_info_utils.cpp.o.d -o CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info_utils.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/smoothing_distance_estimation.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/split_path_constructor.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, false, long unsigned int>]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/split_path_constructor.hpp:104:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' 104 | std::vector common_part = GetCommonPathsEnd(graph_, cur_edge, cur_info.second, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 | (size_t) (cur_info.d() - cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 | (size_t) (cur_info.d() + cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | dijkstra); | ~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:176:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 176 | auto paths = spc.ConvertPIToSplitPaths(e, index_, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 177 | lib_.data().mean_insert_size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 | lib_.data().insert_size_deviation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:63:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 63 | missing_paired_info_count = FillMissing(nthreads); | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:54:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 54 | CorrectPairedInfo(num_threads); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:144:94: required from here 144 | PairInfoImprover(graph, clustered_index, lib, max_repeat_length).ImprovePairedInfo(omp_get_max_threads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp:31:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 31 | size_t min_dist, | ~~~~~~~^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/index_point.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/histogram.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info_buffer.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:8: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'omnigraph::de::PairedIndex::~PairedIndex()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:26:7, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = omnigraph::de::PairedIndex; _Tp = omnigraph::de::PairedIndex]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = omnigraph::de::PairedIndex; _Tp = omnigraph::de::PairedIndex]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = omnigraph::de::PairedIndex; _Up = omnigraph::de::PairedIndex; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1076:24, inlined from '_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = omnigraph::de::PairedIndex*; _ForwardIterator = omnigraph::de::PairedIndex*; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1103:26, inlined from '_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = omnigraph::de::PairedIndex*; _ForwardIterator = omnigraph::de::PairedIndex*; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1145:33, inlined from 'static std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_S_relocate(pointer, pointer, pointer, _Tp_alloc_type&) [with _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:509:26, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const debruijn_graph::DeBruijnGraph&}; _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:647:32: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:17: /usr/include/parallel_hashmap/btree.h: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const debruijn_graph::DeBruijnGraph&}; _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 86%] Linking CXX static library libpath_extend.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack_helpers.cpp [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -MF CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o.d -o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/sequence_mapper_gp_api.cpp [ 87%] Linking CXX static library libpaired_info.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o CMakeFiles/paired_info.dir/paired_info_utils.cpp.o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o /usr/bin/ranlib libpaired_info.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 87%] Built target paired_info In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ [ 87%] Linking CXX static library libpipeline.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 /usr/bin/ar qc libpipeline.a CMakeFiles/pipeline.dir/graph_pack.cpp.o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o CMakeFiles/pipeline.dir/stage.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 87%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o [ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o [ 90%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/read_conversion.cpp [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/construction.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/ss_edge_split.cpp [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/genomic_info_filler.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/subcluster.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/config_struct.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/err_helper_table.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_helpers.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/reference.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/quality_metrics.cpp [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/quality_thresholds_estimator.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/hamcluster_1.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/gamma_poisson_model.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/normal_quality_model.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:92:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 92 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:93:63: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 93 | transition_flow_[nuc][flow] = (1-nuc_avaliability[nuc]) + nuc_avaliability[nuc] * (1-droop_rate) * incomplete_extension_rate; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:104:45: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 104 | int num_flows = read.raw_measurements.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:134:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 134 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:173:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 173 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:357:38: warning: conversion from 'double' to 'float' changes value from '1.0e+20' to '1.00000002e+20f' [-Wfloat-conversion] 357 | float sum_of_squares_upper_bound = 1e20; //max_flows; // Squared distance of solution to measurements | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:416:35: warning: conversion from 'double' to 'float' changes value from '-1.0000000000000001e-1' to '-1.00000001e-1f' [-Wfloat-conversion] 416 | float max_per_flow_metric = -0.1; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:521:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] 521 | child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:33:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 33 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:35:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 35 | num_flows = measurements.size(); | ~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:53:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 53 | unsigned int prefix_size = master_read.sequence.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:299:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 299 | int backward_idx = seq.size()-1; | ~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/hkmer.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/HSeq.hpp: In instantiation of 'static size_t hammer::HSeq::GetDataSize(size_t) [with long unsigned int N = 16; size_t = long unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp:174:52: required from 'void kmers::KMerDiskStorage::merge() [with S = hammer::HSeq<16>; traits = kmers::kmer_index_traits >]' 174 | BucketStorage bucket(*entry, Seq::GetDataSize(k_), false); | ~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp:461:25: required from 'auto kmers::KMerIndexBuilder::BuildIndex(Index&, kmers::KMerCounter&, bool) [with Index = kmers::KMerIndex > >; typename Index::KMerSeq = hammer::HSeq<16>]' 461 | kmer_storage.merge(); | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp:173:102: required from here 173 | auto res = kmers::KMerIndexBuilder(num_files_, cfg::get().max_nthreads).BuildIndex(data.index_, counter, false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/HSeq.hpp:94:36: warning: unused parameter 'size' [-Wunused-parameter] 94 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = adt::identity; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:349:94: required from here 349 | SelfConjugateDisruptor(g_, cfg::get().max_repeat_length, removal_handler_).Run(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:366:28: required from here 366 | cov_cleaner.Run(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:487:24: required from here 487 | CompressAllVertices(gp.get_mutable()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:45:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 45 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:63:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 63 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:85:52: required from here 85 | bool changed = TopologyRemoveErroneousEdges(g_, simplif_cfg_.tec, handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:18: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:107:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 107 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:95:33: required from 'omnigraph::GraphComponent omnigraph::ComplexTipFinder::operator()(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 95 | if (finder.FillDominated()) { | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:150:49: required from 'omnigraph::ComplexTipClipper::ComplexTipClipper(Graph&, double, size_t, size_t, size_t, const std::filesystem::__cxx11::path&, HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 150 | [&](VertexId v) {return !finder_(v).empty();}, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], function, allocator >&)>&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], function, allocator >&)>&}; typename enable_if<(! is_array<_Tp>::value), _Tp>::type = omnigraph::ComplexTipClipper]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:501:65: required from 'omnigraph::AlgoPtr debruijn::simplification::ComplexTipClipperInstance(Graph&, debruijn_graph::config::debruijn_config::simplification::complex_tip_clipper, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 501 | return std::make_shared>(g, ctc_conf.max_relative_coverage, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | ctc_conf.max_edge_len, | ~~~~~~~~~~~~~~~~~~~~~~ 503 | parser.max_length_bound(), info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 504 | "", removal_handler); | ~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:268:42: required from here 268 | ComplexTipClipperInstance(g_, simplif_cfg_.complex_tc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:50:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 50 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; typename enable_if<(! is_array<_Tp>::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:257:57: required from here 257 | RelativeCoverageComponentRemoverInstance(g_, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 258 | simplif_cfg_.rcc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 721 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] 582 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:20: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:812:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 812 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:776:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 776 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:823:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 823 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:792:16: warning: unused variable 'end_height' [-Wunused-variable] 792 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:10: required from here 310 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:32: warning: unused parameter 'v' [-Wunused-parameter] 310 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:321:10: required from here 321 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:323:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 323 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:18: required from here 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:71: warning: unused parameter 'edge2' [-Wunused-parameter] 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here 242 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:245:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 245 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp:91:3: warning: control reaches end of non-void function [-Wreturn-type] 91 | } | ^ [ 92%] Linking CXX executable ../../bin/spades-ionhammer cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-ionhammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-ionhammer.dir/link.d "CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o" "CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o" "CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o" "CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o" "CMakeFiles/spades-ionhammer.dir/main.cpp.o" "CMakeFiles/spades-ionhammer.dir/reference.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o" "CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o" "CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o" "CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-ionhammer ../../common/modules/libmodules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/kmer_index/libmph_index.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/alignment/libalignment.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lssw ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../_deps/zlib_ng-build/libz.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target spades-ionhammer In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:9: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:591:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 92%] Linking CXX static library libstages.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -E cmake_link_script CMakeFiles/stages.dir/link.txt --verbose=1 /usr/bin/ar qc libstages.a CMakeFiles/stages.dir/read_conversion.cpp.o CMakeFiles/stages.dir/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o CMakeFiles/stages.dir/ss_edge_split.cpp.o CMakeFiles/stages.dir/genomic_info_filler.cpp.o /usr/bin/ranlib libstages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Building CXX object common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -MF CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d -o CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/concurrent_dsu.cpp [ 92%] Linking CXX static library libcommon_modules.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/cmake -E cmake_link_script CMakeFiles/common_modules.dir/link.txt --verbose=1 /usr/bin/ar qc libcommon_modules.a CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o /usr/bin/ranlib libcommon_modules.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target common_modules make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/depend make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gfa-split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o [ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o [ 92%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o [ 92%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o [ 92%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o [ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o [ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o [ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o [ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o [ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/positional_read.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/series_analysis.cpp [ 95%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/main.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/config_struct.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o -MF CMakeFiles/spades-kmercount.dir/kmercount.cpp.o.d -o CMakeFiles/spades-kmercount.dir/kmercount.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp [ 95%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hammer_tools.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/main.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/read_filter.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o -MF CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gbuilder.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_data.cpp [ 96%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/mts/contig_abundance.cpp [ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -MF CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o.d -o CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gfa_split.cpp [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/convert_bin_to_fasta.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/interesting_pos_processor.cpp [ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp [ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.cpp.o -MF CMakeFiles/spades-gmapper.dir/gmapper.cpp.o.d -o CMakeFiles/spades-gmapper.dir/gmapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/dataset_processor.cpp [ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o [ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmer_estimating.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/config_struct_hammer.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/cds_subgraphs/profile_storage.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/expander.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp:162:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 162 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp:162:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 162 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp:73:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 73 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:544:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' 544 | vm.Start(vals, num_elems, num_threads); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:55:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' 55 | PairSort::InitAndSort(data.data(), blocks.data(), data.size(), data.size() > 1000*16 ? -1 : 1); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:148:21: required from here 148 | Splitter.split([&] (const std::vector::iterator &start, size_t sz) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | if (sz < block_thr) { | ~~~~~~~~~~~~~~~~~~~~~ 150 | // Merge small blocks. | ~~~~~~~~~~~~~~~~~~~~~~ 151 | processBlockQuadratic(uf, start, sz, data, tau_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 | } else { | ~~~~~~~~ 153 | big_blocks1 += 1; | ~~~~~~~~~~~~~~~~~ 154 | // Otherwise - dump for next iteration. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 | for (unsigned i = 0; i < tau_ + 1; ++i) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 | serialize(bfs, kfs, | ~~~~~~~~~~~~~~~~~~~ 157 | data, &start, sz, | ~~~~~~~~~~~~~~~~~ 158 | SubKMerStridedSerializer(i, tau_ + 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | } | ~ 160 | } | ~ 161 | }); | ~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:401:42: warning: unused parameter 'num_elems' [-Wunused-parameter] 401 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~~~~^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:401:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 401 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp:134:19: warning: unused variable 'mode' [-Wunused-variable] 134 | pipeline_type mode = cfg::get().mode; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp: In function 'void spades::assemble_genome()': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp:236:46: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 236 | graph_pack::GraphPack conj_gp(cfg::get().K, | ~~~~~~~~~~~^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:25: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 329 | while (pref_remove < coverages.size() && coverages[pref_remove] < cov / 2 ) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:485:14: warning: unused variable 'u1' [-Wunused-variable] 485 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:486:14: warning: unused variable 'u2' [-Wunused-variable] 486 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] 659 | size_t cur_len = end_it - start_it; | ^~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp: In function 'void debruijn::simplification::Simplify(graph_pack::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] 103 | const bool using_edge_qual = edge_qual.IsAttached(); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gbuilder.cpp:25: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp:344:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 344 | for (uint32_t j=0; j::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:2995:39: warning: array subscript 6 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 2995 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 48 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3064:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4366:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4395:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:5709:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:5735:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:2995:39: warning: array subscript 7 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 2995 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 56 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3064:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4365:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4396:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:5709:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:5735:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:2995:39: warning: array subscript 'const xxh_unalign64 {aka const long unsigned int}[4]' is partly outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 2995 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset [33, 40] into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3064:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4366:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4396:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:5709:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:5735:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:2995:39: warning: array subscript [5, 6] is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 2995 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset [41, 48] into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3064:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4366:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4398:35, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:5709:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:5735:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:2995:39: warning: array subscript 5 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 2995 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 40 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:752:28: required from here 752 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'constexpr void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr > std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; _NonArray<_Tp> = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:157:65: required from here 157 | algo.AddAlgo(RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 158 | rcc_config(rel_cov_proc_enabled), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | simplif_info, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 721 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] 582 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ [ 98%] Linking CXX executable ../../bin/spades-corrector-core cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-corrector-core.dir/link.d "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-corrector-core [ 98%] Linking CXX executable ../../bin/spades-core cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-convert-bin-to-fasta.dir/link.d "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-convert-bin-to-fasta [ 98%] Linking CXX executable ../../bin/spades-kmer-estimating cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-kmer-estimating.dir/link.d "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-kmer-estimating /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-core.dir/link.d "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/hmm/libhmmercpp.a ../../ext/hmmer/libhmmer.a -lspoa ../../ext/easel/libeasel.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-core [ 98%] Linking CXX executable ../../bin/spades-hammer cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-hammer.dir/link.d "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/kmer_index/libmph_index.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-hammer [ 98%] Linking CXX executable ../../bin/spades-gfa-split cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gfa-split.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-gfa-split.dir/link.d "CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gfa-split ../../common/io/graph/libgraphio.a ../../common/toolchain/libtoolchain.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/binary/libbinary_io.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-gfa-split [ 98%] Linking CXX executable ../../bin/spades-read-filter cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-read-filter.dir/link.d "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-read-filter [100%] Linking CXX executable ../../bin/spades-kmercount cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-kmercount.dir/link.d "CMakeFiles/spades-kmercount.dir/kmercount.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-kmercount [100%] Linking CXX executable ../../bin/spades-gmapper cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-gmapper.dir/link.d "CMakeFiles/spades-gmapper.dir/gmapper.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/hmm/libhmmercpp.a ../../ext/hmmer/libhmmer.a -lspoa ../../ext/easel/libeasel.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-gmapper [100%] Linking CXX executable ../../bin/spades-gbuilder cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-gbuilder.dir/link.d "CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-gbuilder [100%] Linking CXX executable ../../bin/spades-gsimplifier cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gsimplifier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-gsimplifier.dir/link.d "CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o" "CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gsimplifier ../../common/toolchain/libtoolchain.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/binary/libbinary_io.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-gsimplifier make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 debruijn_test make[3]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 44 make -f CMakeFiles/Makefile2 test/debruijn/CMakeFiles/debruijn_test.dir/all make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/DependInfo.cmake "--color=" Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target mimalloc-obj Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target gqf Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target edlib Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target lexy_file Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target version Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target format Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target mph_index Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target coverage_model Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target teamcity_gtest Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/lexy/src/CMakeFiles/lexy_file.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target binary_io make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/kmer_index/CMakeFiles/mph_index.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target zlibstatic Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build [ 0%] Built target edlib [ 4%] Built target mimalloc-obj [ 4%] Built target version [ 4%] Built target gqf [ 6%] Built target format [ 6%] Built target mph_index [ 6%] Built target lexy_file make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 9%] Built target teamcity_gtest make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" [ 9%] Built target coverage_model make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for '_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 11%] Built target binary_io Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". [ 29%] Built target zlibstatic make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend Consolidate compiler generated dependencies of target sequence make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwa.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwt.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/is.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/ksw.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/kthread.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/rle.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/rope.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "ext/bwa/CMakeFiles/bwa.dir/utils.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/faidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". [ 29%] Built target sequence Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target bwa Consolidate compiler generated dependencies of target utils Consolidate compiler generated dependencies of target samtools Consolidate compiler generated dependencies of target llvm-support Consolidate compiler generated dependencies of target graphio make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bwa/CMakeFiles/bwa.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/graph/CMakeFiles/graphio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 36%] Built target bwa make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 45%] Built target utils [ 47%] Built target samtools make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend [ 50%] Built target graphio make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" [ 70%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" Dependencies file "common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/compiler_depend.internal". Dependencies file "common/io/sam/CMakeFiles/samio.dir/read.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/compiler_depend.internal". Dependencies file "common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target samio make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/sam/CMakeFiles/samio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 70%] Built target samio make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/parser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target assembly_graph Consolidate compiler generated dependencies of target input make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 75%] Built target input make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend [ 77%] Built target assembly_graph make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" Dependencies file "common/library/CMakeFiles/library.dir/library.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/compiler_depend.internal". Dependencies file "common/library/CMakeFiles/library.dir/library_data.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target library Consolidate compiler generated dependencies of target alignment make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/library/CMakeFiles/library.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 77%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" [ 79%] Built target alignment make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" Dependencies file "common/configs/CMakeFiles/configs.dir/config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/compiler_depend.internal". Dependencies file "common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target modules Consolidate compiler generated dependencies of target configs make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/configs/CMakeFiles/configs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Built target modules [ 84%] Built target configs make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target paired_info Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target paired_info [ 90%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target pipeline make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 90%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" Dependencies file "common/stages/CMakeFiles/stages.dir/construction.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/simplification.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target stages make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 93%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" Dependencies file "common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target common_modules make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/CMakeFiles/common_modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 93%] Built target common_modules make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn/CMakeFiles/debruijn_test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -MF CMakeFiles/debruijn_test.dir/histogram_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/histogram_test.cpp [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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-I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/overlap_removal_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o -MF CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o.d -o CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:142:26: required from here 142 | helper.DeleteLink(vertex, out_edge); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp: In function 'void CheckGFAInOut(const std::string&, const std::string&, const std::filesystem::__cxx11::path&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:63:17: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 63 | Graph graph(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:73:21: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 73 | Graph gfa_graph(K); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp:85:57: required from here 85 | for (auto it = g.SmartVertexBegin(); !it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:23:12: warning: unused variable 'read_count' [-Wunused-variable] 23 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::Point&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:30:12: warning: unused variable 'read_count' [-Wunused-variable] 30 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadGraph(const std::string&, debruijn_graph::Graph&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:69:26: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 69 | VertexId new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), vid, conj_vid); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:127:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 127 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const std::string&, omnigraph::EdgesPositionHandler&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:192:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] 192 | int read_count = fscanf(file, "%zu\n", &pos_count); | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:51:38: required from here 51 | for (size_t i = 0; i < 5; ++i, ++it) | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:38:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' 38 | ++it1; | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:95:26: required from here 95 | CompareGraphIterators(graph.SmartEdgeBegin(), new_graph.SmartEdgeBegin()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp: In function 'void CheckIndex(const std::vector >&, const std::filesystem::__cxx11::path&, size_t)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp:68:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 68 | graph_pack::GraphPack gp(k, tmpdir, 0); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:91:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 91 | Graph g(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:103:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 103 | gap_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:114:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 114 | ends_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:142:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 142 | Graph g(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:152:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 152 | if (g.int_id(e) == eid_int) { | ~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:173:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 173 | Graph g(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:182:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 182 | if (g.int_id(e) == eid_int) { | ~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:190:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 190 | gap_cfg.penalty_ratio = 0.1; | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/paired_info_test.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:49:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 49 | for (auto it = graph_.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:174:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' 174 | this->value_.Remove(this->GetRandomEdge()); | ~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:185:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' 185 | RemoveRandomEdgeInfo(); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:177:10: required from here 177 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:41:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 41 | ++it; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:101:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' 101 | this->value_.AddEdge(this->GetRandomVertex(), this->GetRandomVertex(), | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:120:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' 120 | AddRandomEdge(); | ^~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:113:10: required from here 113 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp: In function 'void test_utils::AssertGraph(size_t, const std::vector >&, const std::vector >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:131:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 131 | Graph g(k); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp: In function 'void test_utils::AssertGraph(size_t, const std::vector, std::__cxx11::basic_string > >&, size_t, size_t, const std::vector >&, const CoverageInfo&, const EdgePairInfo&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:193:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 193 | graph_pack::GraphPack gp(k, "tmp", 1); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:276:16: required from here 276 | remover.Run(); | ~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:45:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 45 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:63:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 63 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:223:72: required from here 223 | while(debruijn::simplification::TopologyRemoveErroneousEdges(g, tec_config, 0)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:122:55: required from here 122 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'constexpr void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr > std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; _NonArray<_Tp> = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:313:83: required from here 313 | auto algo = debruijn::simplification::RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 314 | standard_rcc_config(), | ~~~~~~~~~~~~~~~~~~~~~~ 315 | standard_simplif_relevant_info()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_visualizer.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/path_extend_test.cpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 721 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] 582 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/perf/perfcounter.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:10: In static member function 'static void std::__copy_move::__assign_one(_Tp*, _Up*) [with _Tp = long unsigned int; _Up = const long unsigned int]', inlined from 'static constexpr _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const long unsigned int; _Up = long unsigned int; bool _IsMove = false]' at /usr/include/c++/14/bits/stl_algobase.h:455:20, inlined from 'constexpr _OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from 'constexpr _OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from 'constexpr _OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from 'constexpr _OI std::copy(_II, _II, _OI) [with _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from 'constexpr _ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*; _Tp = long unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'constexpr void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const long unsigned int*; _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1697:33, inlined from 'constexpr std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:682:21, inlined from 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:133:51: /usr/include/c++/14/bits/stl_algobase.h:413:17: warning: 'split_link' may be used uninitialized [-Wmaybe-uninitialized] 413 | { *__to = *__from; } | ~~~~~~^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp: In function 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:124:20: note: 'split_link' was declared here 124 | LinkId split_link; | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:107:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 107 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:989:43: required from 'omnigraph::complex_br::LocalizedComponentFinder::LocalizedComponentFinder(const Graph&, size_t, size_t, VertexId) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; VertexId = omnigraph::impl::VertexId]' 989 | dominated_set_finder.FillDominated(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1058:41: required from 'bool omnigraph::complex_br::CandidateFinder::Check(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1058 | LocalizedComponentFinder comp_finder(g, max_length_, | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1056:10: required from here 1056 | bool Check(VertexId v) const override { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:50:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 50 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:20: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:812:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 812 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:776:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 776 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:823:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 823 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:792:16: warning: unused variable 'end_height' [-Wunused-variable] 792 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:821:43: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 821 | gc.e_end()); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:10: required from here 310 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:32: warning: unused parameter 'v' [-Wunused-parameter] 310 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:321:10: required from here 321 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:323:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 323 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:18: required from here 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:71: warning: unused parameter 'edge2' [-Wunused-parameter] 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here 242 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:245:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 245 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:8: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'constexpr void std::allocator< >::deallocate(_Tp*, std::size_t) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]' at /usr/include/c++/14/bits/allocator.h:208:35, inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:536:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'constexpr void std::destroy_at(_Tp*) [with _Tp = pair > >, phmap::Less, allocator > > > > > > >]' at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from 'static constexpr void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:593:19, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [100%] Linking CXX executable ../../bin/debruijn_test cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/cmake -E cmake_link_script CMakeFiles/debruijn_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/debruijn_test.dir/link.d CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o CMakeFiles/debruijn_test.dir/test_utils.cpp.o CMakeFiles/debruijn_test.dir/construction_test.cpp.o CMakeFiles/debruijn_test.dir/io_test.cpp.o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o CMakeFiles/debruijn_test.dir/graphio.cpp.o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o CMakeFiles/debruijn_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/debruijn_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/teamcity_gtest/libteamcity_gtest.a -lgtest ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a -lm ../../_deps/zlib_ng-build/libz.a ../../ext/lexy/src/liblexy_file.a make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/kmer_index/CMakeFiles/mph_index.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for '_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build [ 2%] Built target mimalloc-obj [ 4%] Built target format [ 4%] Built target mph_index [ 4%] Built target edlib [ 4%] Built target gqf [ 7%] Built target version make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend [ 9%] Built target teamcity_gtest [ 9%] Built target coverage_model make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" [ 11%] Built target binary_io make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" [ 30%] Built target zlibstatic make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 52%] Built target llvm-support make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bwa/CMakeFiles/bwa.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 52%] Built target sequence [ 54%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend [ 64%] Built target samtools make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend [ 71%] Built target bwa make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/sam/CMakeFiles/samio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 71%] Built target samio make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend [ 73%] Built target assembly_graph make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Built target input make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" [ 80%] Built target alignment make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/library/CMakeFiles/library.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build [ 80%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" [ 83%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/configs/CMakeFiles/configs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build [ 85%] Built target configs make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/CMakeFiles/common_modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target common_modules make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test/CMakeFiles/include_test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/sequence_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/quality_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/cyclic_hash_test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/nucl_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/binary_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/test.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:8: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:462:26, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:157:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:68: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:156:12: note: 's1$_M_elems$' was declared here 156 | Seq<7> s1("ACGTACT"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:462:26, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:160:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:68: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:159:12: note: 's2$_M_elems$' was declared here 159 | Seq<7> s2("TTTTTTT"); | ^~ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'virtual void Seq_ShiftLeft_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:28:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftLeft_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:27:13: note: 's$_M_elems$' was declared here 27 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'Seq Seq::operator>>(char) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'virtual void Seq_ShiftRight_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:41:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:342:42: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 342 | res.data_[i] = (res.data_[i] << 2) | rm; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftRight_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:40:13: note: 's$_M_elems$' was declared here 40 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void Seq_Str_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:55:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Str_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:54:13: note: 's$_M_elems$' was declared here 54 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<10>; long unsigned int size_ = 9; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'virtual void Seq_HeadAndTail_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:62:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_HeadAndTail_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:61:13: note: 's$_M_elems$' was declared here 61 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'void Seq::set(size_t, char) [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq Seq::operator!() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:241:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:138:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:358:40: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 358 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:137:13: note: 's$_M_elems$' was declared here 137 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'void Seq::set(size_t, char) [with long unsigned int size_ = 9; T = long unsigned int]', inlined from 'Seq Seq::operator!() const [with long unsigned int size_ = 9; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:241:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:142:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:358:40: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 358 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:141:12: note: 's3$_M_elems$' was declared here 141 | Seq<9> s3("ACGTACGTA"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<10>; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'virtual void Seq_FromBiggerSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:68:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_FromBiggerSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:67:13: note: 's$_M_elems$' was declared here 67 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<5>; long unsigned int size_ = 4; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'Seq Seq::end() const [with long unsigned int size2_ = 4; T2 = long unsigned int; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:445:16, inlined from 'virtual void Seq_End_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:116:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_End_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:115:12: note: 's1$_M_elems$' was declared here 115 | Seq<5> s1("ACGTA"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<5>; long unsigned int size_ = 4; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'Seq Seq::start() const [with long unsigned int size2_ = 4; T2 = long unsigned int; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:439:16, inlined from 'virtual void Seq_Start_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:121:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Start_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:120:12: note: 's1$_M_elems$' was declared here 120 | Seq<5> s1("ACGTA"); | ^~ In member function 'Seq<(size_ + 1), T> Seq::pushBack(char) const [with long unsigned int size_ = 4; T = long unsigned int]', inlined from 'virtual void Seq_PushBack_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:80:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:288:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 288 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:79:16: note: 's$_M_elems$' was declared here 79 | Seq<4> s("ACGT"); | ^ In file included from /usr/include/gtest/gtest.h:71, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:84:38: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 84 | EXPECT_EQ("ACGTC", s.pushBack('C').str()); | ~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:83:31: note: 's$_M_elems$' was declared here 83 | Seq<4, unsigned char> s("ACGT"); | ^ In member function 'Seq<(size_ + 1), T> Seq::pushBack(char) const [with long unsigned int size_ = 3; T = long unsigned int]', inlined from 'virtual void Seq_PushBack_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:88:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:288:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 288 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:87:16: note: 's$_M_elems$' was declared here 87 | Seq<3> s("ACG"); | ^ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'virtual void Seq_Test16_2_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:152:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_2_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:151:13: note: 's$_M_elems$' was declared here 151 | Seq<16> s("TTTTTTTTTTTTTTTT"); | ^ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'virtual void Seq_Test16_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:147:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:146:13: note: 's$_M_elems$' was declared here 146 | Seq<16> s("AAAAAAAAAAAAAAAA"); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:20, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:8: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:337:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:329:12: note: 's$_M_elems$' was declared here 329 | Seq<5> s("CGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:338:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:330:13: note: 's1$_M_elems$' was declared here 330 | Seq<10> s1("ACGTACGTAC"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 16; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:339:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:331:13: note: 's2$_M_elems$' was declared here 331 | Seq<16> s2("CCCCGTACGTACGTAC"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 32; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 32; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:340:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:332:13: note: 's3$_M_elems$' was declared here 332 | Seq<32> s3("ACGTACGTACACGTACGTACACGTACGTACAC"); | ^~ [100%] Linking CXX executable ../../bin/include_test cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/cmake -E cmake_link_script CMakeFiles/include_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/include_test.dir/link.d CMakeFiles/include_test.dir/seq_test.cpp.o CMakeFiles/include_test.dir/sequence_test.cpp.o CMakeFiles/include_test.dir/rtseq_test.cpp.o CMakeFiles/include_test.dir/quality_test.cpp.o CMakeFiles/include_test.dir/nucl_test.cpp.o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o CMakeFiles/include_test.dir/binary_test.cpp.o CMakeFiles/include_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/include_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/teamcity_gtest/libteamcity_gtest.a -lgtest ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target include_test make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_test -O--sourcedirectory=src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: include_test 1: Test command: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/bin/include_test 1: Working Directory: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test 1: Test timeout computed to be: 10000000 test 2 Start 2: debruijn_test 2: Test command: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/bin/debruijn_test 2: Working Directory: /build/reproducible-path/spades-4.0.0+dfsg1/src/.. 2: Test timeout computed to be: 10000000 1: Running main() from gtest_main.cpp 1: [==========] Running 58 tests from 7 test suites. 1: [----------] Global test environment set-up. 1: [----------] 20 tests from Seq 1: [ RUN ] Seq.Selector 1: [ OK ] Seq.Selector (0 ms) 1: [ RUN ] Seq.ShiftLeft 1: [ OK ] Seq.ShiftLeft (0 ms) 1: [ RUN ] Seq.ShiftRight 1: [ OK ] Seq.ShiftRight (0 ms) 1: [ RUN ] Seq.Str 1: [ OK ] Seq.Str (0 ms) 1: [ RUN ] Seq.HeadAndTail 1: [ OK ] Seq.HeadAndTail (0 ms) 1: [ RUN ] Seq.FromBiggerSeq 1: [ OK ] Seq.FromBiggerSeq (0 ms) 1: [ RUN ] Seq.FromType 1: [ OK ] Seq.FromType (0 ms) 1: [ RUN ] Seq.PushBack 1: [ OK ] Seq.PushBack (0 ms) 1: [ RUN ] Seq.Null 1: [ OK ] Seq.Null (0 ms) 1: [ RUN ] Seq.EndNull 1: [ OK ] Seq.EndNull (0 ms) 1: [ RUN ] Seq.StartNull 1: [ OK ] Seq.StartNull (0 ms) 1: [ RUN ] Seq.AddSymbolForNullValue 1: [ OK ] Seq.AddSymbolForNullValue (0 ms) 1: [ RUN ] Seq.End 1: [ OK ] Seq.End (0 ms) 1: [ RUN ] Seq.Start 1: [ OK ] Seq.Start (0 ms) 1: [ RUN ] Seq.Complex 1: [ OK ] Seq.Complex (0 ms) 1: [ RUN ] Seq.FromCharArray 1: [ OK ] Seq.FromCharArray (0 ms) 1: [ RUN ] Seq.ReverseComplement 1: [ OK ] Seq.ReverseComplement (0 ms) 1: [ RUN ] Seq.Test16 1: [ OK ] Seq.Test16 (0 ms) 1: [ RUN ] Seq.Test16_2 1: [ OK ] Seq.Test16_2 (0 ms) 1: [ RUN ] Seq.TestFirstLast 1: [ OK ] Seq.TestFirstLast (0 ms) 1: [----------] 20 tests from Seq (0 ms total) 1: 1: [----------] 6 tests from Sequence 1: [ RUN ] Sequence.Selector 1: [ OK ] Sequence.Selector (0 ms) 1: [ RUN ] Sequence.ZeroLength 1: [ OK ] Sequence.ZeroLength (0 ms) 1: [ RUN ] Sequence.NullValue 1: [ OK ] Sequence.NullValue (0 ms) 1: [ RUN ] Sequence.Sum 1: [ OK ] Sequence.Sum (0 ms) 1: [ RUN ] Sequence.Str 1: [ OK ] Sequence.Str (0 ms) 1: [ RUN ] Sequence.ReverseComplement 1: [ OK ] Sequence.ReverseComplement (0 ms) 1: [----------] 6 tests from Sequence (0 ms total) 1: 1: [----------] 23 tests from RtSeq 1: [ RUN ] RtSeq.Selector 1: [ OK ] RtSeq.Selector (0 ms) 1: [ RUN ] RtSeq.ShiftLeft 1: [ OK ] RtSeq.ShiftLeft (0 ms) 1: [ RUN ] RtSeq.ShiftLeftThis 1: [ OK ] RtSeq.ShiftLeftThis (0 ms) 1: [ RUN ] RtSeq.ShiftRight 1: [ OK ] RtSeq.ShiftRight (0 ms) 1: [ RUN ] RtSeq.ShiftRightThis 1: [ OK ] RtSeq.ShiftRightThis (0 ms) 1: [ RUN ] RtSeq.Str 1: [ OK ] RtSeq.Str (0 ms) 1: [ RUN ] RtSeq.HeadAndTail 1: [ OK ] RtSeq.HeadAndTail (0 ms) 1: [ RUN ] RtSeq.FromBiggerRtSeq 1: [ OK ] RtSeq.FromBiggerRtSeq (0 ms) 1: [ RUN ] RtSeq.FromSeq 1: [ OK ] RtSeq.FromSeq (0 ms) 1: [ RUN ] RtSeq.ToSeq 1: [ OK ] RtSeq.ToSeq (0 ms) 1: [ RUN ] RtSeq.FromType 1: [ OK ] RtSeq.FromType (0 ms) 1: [ RUN ] RtSeq.PushBack 1: [ OK ] RtSeq.PushBack (0 ms) 1: [ RUN ] RtSeq.PushBackThis 1: [ OK ] RtSeq.PushBackThis (0 ms) 1: [ RUN ] RtSeq.PushFront 1: [ OK ] RtSeq.PushFront (0 ms) 1: [ RUN ] RtSeq.PushFrontThis 1: [ OK ] RtSeq.PushFrontThis (0 ms) 1: [ RUN ] RtSeq.Null 1: [ OK ] RtSeq.Null (0 ms) 1: [ RUN ] RtSeq.AddSymbolForNullValue 1: [ OK ] RtSeq.AddSymbolForNullValue (0 ms) 1: [ RUN ] RtSeq.Complex 1: [ OK ] RtSeq.Complex (0 ms) 1: [ RUN ] RtSeq.FromCharArray 1: [ OK ] RtSeq.FromCharArray (0 ms) 1: [ RUN ] RtSeq.ReverseComplement 1: [ OK ] RtSeq.ReverseComplement (0 ms) 1: [ RUN ] RtSeq.16 1: [ OK ] RtSeq.16 (0 ms) 1: [ RUN ] RtSeq.16_2 1: [ OK ] RtSeq.16_2 (0 ms) 1: [ RUN ] RtSeq.FirstLast 1: [ OK ] RtSeq.FirstLast (0 ms) 1: [----------] 23 tests from RtSeq (0 ms total) 1: 1: [----------] 1 test from Quality 1: [ RUN ] Quality.Test 1: [ OK ] Quality.Test (0 ms) 1: [----------] 1 test from Quality (0 ms total) 1: 1: [----------] 1 test from Nucl 1: [ RUN ] Nucl.Test 1: [ OK ] Nucl.Test (0 ms) 1: [----------] 1 test from Nucl (0 ms total) 1: 1: [----------] 4 tests from CyclicHash 1: [ RUN ] CyclicHash.TestBasic 1: [ OK ] CyclicHash.TestBasic (0 ms) 1: [ RUN ] CyclicHash.TestBasicRtSeq 1: [ OK ] CyclicHash.TestBasicRtSeq (0 ms) 1: [ RUN ] CyclicHash.TestRC 1: [ OK ] CyclicHash.TestRC (0 ms) 1: [ RUN ] CyclicHash.TestRoll 1: [ OK ] CyclicHash.TestRoll (0 ms) 1: [----------] 4 tests from CyclicHash (0 ms total) 1: 1: [----------] 3 tests from Binary 1: [ RUN ] Binary.Simple 1: [ OK ] Binary.Simple (0 ms) 1: [ RUN ] Binary.Containers 1: [ OK ] Binary.Containers (0 ms) 1: [ RUN ] Binary.Variadic 1: [ OK ] Binary.Variadic (0 ms) 1: [----------] 3 tests from Binary (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 58 tests from 7 test suites ran. (0 ms total) 1: [ PASSED ] 58 tests. 1/2 Test #1: include_test ..................... Passed 0.00 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 100 tests from 11 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.Empty (0 ms) 2: [ RUN ] GraphCore.OneVertex 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) 2: [----------] 6 tests from GraphCore (0 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic 2: [ OK ] Histogram.StrongWeakPtrBasic (0 ms) 2: [----------] 1 test from Histogram (0 ms total) 2: 2: [----------] 13 tests from PairedInfo 2: [ RUN ] PairedInfo.Construct 2: [ OK ] PairedInfo.Construct (0 ms) 2: [ RUN ] PairedInfo.Access 2: [ OK ] PairedInfo.Access (0 ms) 2: [ RUN ] PairedInfo.HalfAccess 2: [ OK ] PairedInfo.HalfAccess (0 ms) 2: [ RUN ] PairedInfo.Remove 2: [ OK ] PairedInfo.Remove (0 ms) 2: [ RUN ] PairedInfo.UnexistingEdges 2: [ OK ] PairedInfo.UnexistingEdges (0 ms) 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours 2: [ OK ] PairedInfo.Neighbours (0 ms) 2: [ RUN ] PairedInfo.DoubledInfo 2: [ OK ] PairedInfo.DoubledInfo (0 ms) 2: [ RUN ] PairedInfo.HalfNeighbours 2: [ OK ] PairedInfo.HalfNeighbours (0 ms) 2: [ RUN ] PairedInfo.MoreNeighbours 2: [ OK ] PairedInfo.MoreNeighbours (0 ms) 2: [ RUN ] PairedInfo.Merge 2: [ OK ] PairedInfo.Merge (0 ms) 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] PairedInfo.RandomSymmetry (37 ms) 2: [----------] 13 tests from PairedInfo (37 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Trivial (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch2 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch2 (0 ms) 2: [ RUN ] OverlapAnalysis.Deletion 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Deletion (0 ms) 2: [ RUN ] OverlapAnalysis.Insertion 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Insertion (0 ms) 2: [ RUN ] OverlapAnalysis.QueryLonger 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.QueryLonger (0 ms) 2: [ RUN ] OverlapAnalysis.RefLonger 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.RefLonger (0 ms) 2: [ RUN ] OverlapAnalysis.TrivialBoundedFlank 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.TrivialBoundedFlank (0 ms) 2: [ RUN ] OverlapAnalysis.PartialPerfectAlignment 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.PartialPerfectAlignment (0 ms) 2: [ RUN ] OverlapAnalysis.Unalignable 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Unalignable (0 ms) 2: [ RUN ] OverlapAnalysis.Large 2: [ OK ] OverlapAnalysis.Large (0 ms) 2: [ RUN ] OverlapAnalysis.SimpleGap 2: [ OK ] OverlapAnalysis.SimpleGap (0 ms) 2: [ RUN ] OverlapAnalysis.UndefinedBehavior 2: [ OK ] OverlapAnalysis.UndefinedBehavior (0 ms) 2: [----------] 13 tests from OverlapAnalysis (0 ms total) 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest 2: 0:00:00.038 1M / 11M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.038 1M / 11M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.039 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp 2: 0:00:00.039 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started 2: 0:00:00.039 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip 2: [ OK ] Simplification.SimpleTipClipperTest (1 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest 2: 0:00:00.040 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.040 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.040 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp 2: 0:00:00.040 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.040 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.040 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (0 ms) 2: [ RUN ] Simplification.TipobulgeTest 2: 0:00:00.041 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.041 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.041 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest 2: 0:00:00.041 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.041 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.060 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleECTest (61 ms) 2: [ RUN ] Simplification.SimpleIterECTest 2: 0:00:00.103 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.103 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.103 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.103 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.118 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleIterECTest (57 ms) 2: [ RUN ] Simplification.IterECTest 2: 0:00:00.160 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.160 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.160 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.160 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.175 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.IterECTest (56 ms) 2: [ RUN ] Simplification.IterUniquePath 2: 0:00:00.217 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.217 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.217 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.217 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.231 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: 0:00:00.231 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: 0:00:00.239 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: [ OK ] Simplification.IterUniquePath (63 ms) 2: [ RUN ] Simplification.MFUniquePath 2: 0:00:00.281 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.281 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.281 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp 2: 0:00:00.281 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started 2: 0:00:00.291 606M / 606M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path 2: 0:00:00.291 606M / 606M INFO General (single_cell_simplification: 133) Removing connections based on max flow strategy 2: [ OK ] Simplification.MFUniquePath (66 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge 2: 0:00:00.347 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.347 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.347 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp 2: 0:00:00.347 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.347 1M / 50M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.348 1M / 50M INFO General (simplification_test.cpp : 277) Done 2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (1 ms) 2: [ RUN ] Simplification.ComplexBulge 2: 0:00:00.348 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.348 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.348 1M / 50M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.348 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:00.348 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.362 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.362 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.388 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.442 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). 2: 0:00:00.442 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.469 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.469 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: [ OK ] Simplification.ComplexBulge (199 ms) 2: [ RUN ] Simplification.BigComplexBulge 2: 0:00:00.547 1M / 55M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.547 1M / 55M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.547 1M / 55M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.548 1M / 55M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp 2: 0:00:00.548 1M / 55M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:00.641 1160M / 1160M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: 0:00:00.642 1160M / 1160M INFO General (edge_index.hpp : 175) Using small index (max_id = 21667994) 2: 0:00:00.660 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.682 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). 2: 0:00:00.682 1161M / 1161M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.708 1161M / 1161M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:00.708 1161M / 1161M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: [ OK ] Simplification.BigComplexBulge (239 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover 2: 0:00:00.787 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.787 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.787 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.787 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp 2: 0:00:00.787 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:00.788 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.788 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 3036) 2: 0:00:00.792 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.816 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). 2: 0:00:00.816 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.828 2M / 159M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:00.828 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.828 2M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover (81 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 2: 0:00:00.868 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.868 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.868 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.868 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:00.868 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.884 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.884 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.910 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.963 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). 2: 0:00:00.963 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.991 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.991 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.991 1172M / 1172M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover1 (200 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 2: 0:00:01.069 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.069 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.069 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.069 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp 2: 0:00:01.069 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started 2: 0:00:01.069 3M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:01.069 3M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 35260) 2: 0:00:01.069 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.071 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). 2: 0:00:01.071 3M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.071 3M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.071 3M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:01.071 3M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover2 (10 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 2: 0:00:01.080 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.080 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.080 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.080 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:01.080 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:01.080 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.080 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 12354) 2: 0:00:01.080 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.080 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). 2: 0:00:01.080 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.081 1M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.081 1M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.081 1M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover3 (2 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 2: 0:00:01.082 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.082 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.082 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.082 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp 2: 0:00:01.082 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started 2: 0:00:01.082 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:01.082 4M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 36400) 2: 0:00:01.083 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.086 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). 2: 0:00:01.087 4M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.088 4M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.088 4M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:01.088 4M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover4 (19 ms) 2: [ RUN ] Simplification.CompressorTest 2: 0:00:01.101 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.101 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.101 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.101 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp 2: 0:00:01.101 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started 2: 0:00:01.101 2M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: 0:00:01.101 2M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 5512) 2: 0:00:01.101 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.102 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). 2: 0:00:01.102 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.102 2M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.102 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: [ OK ] Simplification.CompressorTest (1 ms) 2: [----------] 17 tests from Simplification (1064 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread 2: 0:00:01.102 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.102 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.103 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.103 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.103 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.103 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.103 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.107 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 2 reads 2: 0:00:01.107 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.109 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:01.109 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.109 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.109 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.109 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.109 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.112 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 6 kmers. 2: 0:00:01.112 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.113 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 7 kmers in total. 2: 0:00:01.113 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.114 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). 2: 0:00:01.114 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.114 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.114 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.114 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.115 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.115 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:01.115 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.115 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.115 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.115 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.115 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread (13 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 2: 0:00:01.116 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.116 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.116 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.116 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.116 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.116 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.117 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.120 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.120 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.121 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8 kmers in total. 2: 0:00:01.121 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.121 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.121 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.121 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.121 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.124 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 8 kmers. 2: 0:00:01.124 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.126 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 9 kmers in total. 2: 0:00:01.126 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.126 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). 2: 0:00:01.126 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.127 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.127 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.127 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.127 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.127 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread2 (11 ms) 2: [ RUN ] GraphConstruction.SplitThread 2: 0:00:01.128 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.128 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.128 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.128 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.128 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.128 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.128 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.131 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.131 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.133 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:01.133 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.133 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.133 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.133 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.133 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.136 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:01.136 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.137 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:01.137 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.138 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:01.138 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.138 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.138 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.139 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.139 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.139 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.139 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.139 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.139 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.139 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:01.139 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread (11 ms) 2: [ RUN ] GraphConstruction.SplitThread2 2: 0:00:01.139 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.139 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.139 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.139 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.139 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.139 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.139 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.143 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.143 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.144 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:01.144 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.144 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.144 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.144 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.144 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.147 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:01.147 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.149 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:01.149 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.149 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). 2: 0:00:01.149 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.150 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.150 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.150 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.150 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.150 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 4 sequences extracted 2: 0:00:01.150 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.150 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.150 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.150 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 8 edges to create 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:01.150 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread2 (11 ms) 2: [ RUN ] GraphConstruction.Buldge 2: 0:00:01.151 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.151 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.151 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.151 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.151 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.151 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.151 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.154 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.154 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.155 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:01.155 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.156 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.156 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.156 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.156 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.159 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 12 kmers. 2: 0:00:01.159 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.160 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:01.160 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.161 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:01.161 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.161 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.161 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.161 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.161 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.162 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2 sequences extracted 2: 0:00:01.162 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.162 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.162 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.162 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 4 edges to create 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.162 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.Buldge (11 ms) 2: [ RUN ] GraphConstruction.CondenseSimple 2: 0:00:01.162 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.162 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.162 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.162 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.162 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.162 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.162 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.166 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.166 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.167 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.167 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.167 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.167 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.167 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.167 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.170 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.170 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.172 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.172 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.172 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:01.172 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.173 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.173 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.173 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.173 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.173 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.173 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.173 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.173 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.173 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.173 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.CondenseSimple (11 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex 2: 0:00:01.174 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.174 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.174 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.174 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.174 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.174 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.174 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.174 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.177 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.177 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.179 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.179 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.179 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.179 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.179 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.179 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.182 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.182 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.183 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.183 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.184 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:01.184 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.185 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.185 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.185 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.185 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.185 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.185 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.185 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.185 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.185 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.185 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.185 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.185 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:01.185 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.185 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:01.185 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerStoringIndex (11 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex 2: 0:00:01.186 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.186 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.186 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.186 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.186 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.186 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.186 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.186 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.189 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.189 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.190 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.190 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.190 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.190 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.191 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.191 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.194 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.194 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.195 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.195 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.196 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:01.196 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.196 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.197 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.197 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.197 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.197 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.197 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.197 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.197 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.197 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.197 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.197 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.197 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:01.197 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.197 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:01.197 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerFreeIndex (11 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo 2: 0:00:01.197 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.197 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.197 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.198 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=3 2: 0:00:01.198 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.198 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.198 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.198 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.201 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.201 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.202 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 5 kmers in total. 2: 0:00:01.202 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.202 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.202 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.202 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.202 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.205 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 5 kmers. 2: 0:00:01.206 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.207 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:01.207 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.207 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). 2: 0:00:01.207 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.208 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.208 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.208 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.208 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.208 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 5 sequences extracted 2: 0:00:01.208 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.208 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.208 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.208 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 10 edges to create 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 6 vertices to create 2: 0:00:01.208 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.208 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.208 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 13) 2: 0:00:01.208 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.208 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). 2: 0:00:01.208 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.208 1M / 159M INFO General (graph_construction.hpp : 94) Filling coverage index 2: 0:00:01.208 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.209 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). 2: 0:00:01.209 1M / 159M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. 2: 0:00:01.209 1M / 159M INFO General (graph_construction.hpp : 100) Filling coverage and flanking coverage from PHM 2: 0:00:01.209 1M / 159M INFO General (graph_pack_helpers.cpp : 54) Normalizing k-mer map. Total 0 kmers to process 2: 0:00:01.209 1M / 159M INFO General (graph_pack_helpers.cpp : 56) Normalizing done 2: 0:00:01.212 14M / 159M INFO General (sequence_mapper_notifier.h: 64) Starting sequence mapping 2: 0:00:01.214 14M / 159M INFO General (sequence_mapper_notifier.h: 103) Total 2 reads processed 2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (19 ms) 2: [----------] 9 tests from GraphConstruction (114 ms total) 2: 2: [----------] 4 tests from Io 2: [ RUN ] Io.Order 2: 0:00:01.217 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.217 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.252 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.252 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.Order (35 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (3 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [ RUN ] Io.GFADBG 2: 0:00:01.256 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.256 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.256 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:01.256 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:01.256 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.257 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.257 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.257 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.257 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.257 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp.grp 2: 0:00:01.257 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp started 2: 0:00:01.258 49M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/topology_ec/self_comp 2: 0:00:01.260 49M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.260 49M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.GFADBG (6 ms) 2: [----------] 4 tests from Io (45 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor 2: 0:00:01.263 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.263 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.263 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.263 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.263 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathConstructor (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove 2: 0:00:01.263 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.263 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.263 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.263 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch 2: 0:00:01.265 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.265 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector 2: 0:00:01.265 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.265 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) 2: [----------] 8 tests from PathExtend (2 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff 2: 0:00:01.265 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.265 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.265 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicNoDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicDiff 2: 0:00:01.266 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.266 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges 2: 0:00:01.266 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.266 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: 0:00:01.266 1M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat 2: 0:00:01.266 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.266 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.266 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.271 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.271 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeat (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven 2: 0:00:01.271 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.272 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.272 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.272 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.276 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.276 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatUneven (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.281 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.281 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.281 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect 2: 0:00:01.281 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.281 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.281 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.281 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.286 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.286 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd 2: 0:00:01.286 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.286 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.286 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.286 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.290 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.290 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.290 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEnd (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain 2: 0:00:01.291 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.291 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.291 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.291 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.295 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.295 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.295 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart 2: 0:00:01.295 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.295 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.295 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.295 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.300 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.300 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.300 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStart (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain 2: 0:00:01.300 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.300 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.300 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.300 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.304 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.305 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.305 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (4 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication 2: 0:00:01.305 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.305 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.305 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.305 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.309 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplication (4 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual 2: 0:00:01.309 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.310 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.310 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.310 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.314 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff 2: 0:00:01.314 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.314 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.314 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.314 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.319 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiff (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap 2: 0:00:01.319 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.319 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.319 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.319 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.323 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiffGap (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 2: 0:00:01.323 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.324 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.324 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.324 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.328 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 2: 0:00:01.328 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.328 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.328 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.328 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.333 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (4 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen 2: 0:00:01.333 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.333 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.333 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.333 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.337 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.337 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.337 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.Tricky0 2: 0:00:01.338 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.338 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.338 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.338 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.342 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.342 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.342 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky0 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky1 2: 0:00:01.342 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.342 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.342 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.342 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.347 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.347 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.347 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky1 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky2 2: 0:00:01.347 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.347 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.347 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.347 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.351 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.352 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.352 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky2 (4 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen 2: 0:00:01.352 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.352 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.352 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.352 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.356 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.356 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.356 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle 2: 0:00:01.357 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.357 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.357 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.357 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.361 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.361 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.361 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.OverlapWithMiddle (4 ms) 2: [----------] 23 tests from OverlapRemoval (96 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest 2: 0:00:01.361 1M / 159M INFO General (graph_alignment_test.cpp : 31) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero 2: 0:00:01.361 1M / 159M INFO General (graph_alignment_test.cpp : 61) Edlib: Result status = 0 2: 0:00:01.361 1M / 159M INFO General (graph_alignment_test.cpp : 63) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest 2: 0:00:01.361 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.361 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.361 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.361 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.366 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.366 4M / 159M INFO BWAIndex (bwa_index.cpp : 52) Setting BWA alignment mode to 'pacbio' 2: 0:00:01.371 5M / 159M INFO General (bwa_index.cpp : 150) Using BWA IS algorithm 2: [ OK ] GraphAligner.TrivialTest (433 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest 2: 0:00:01.795 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.795 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.795 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.795 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.799 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraOneEdgeTest (4 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest 2: 0:00:01.800 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.800 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.800 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.800 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.804 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (4 ms) 2: [----------] 5 tests from GraphAligner (443 ms total) 2: 2: [----------] 1 test from VariableOverlaps 2: [ RUN ] VariableOverlaps.BasicOperations 2: 0:00:01.805 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.805 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.805 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.805 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] VariableOverlaps.BasicOperations (0 ms) 2: [----------] 1 test from VariableOverlaps (0 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 100 tests from 11 test suites ran. (1805 ms total) 2: [ PASSED ] 100 tests. 2/2 Test #2: debruijn_test .................... Passed 1.81 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.82 sec make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src -O--buildsystem=cmake dh_prep -O--sourcedirectory=src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/spades-4.0.0\+dfsg1/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-bwa -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-corrector-core -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/corrector -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/corrector/corrector.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-hammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/hammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/hammer/config.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-ionhammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/ionhammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/ionhammer/ionhammer.cfg -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/config.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/sewage_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/pe_params.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/toy.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/simplification.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/sewage -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/sewage/usher_barcodes.csv -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/plasmidspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/rnaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaviralspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaplasmidspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/rnaviralspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/coronaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades_init.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executors.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_local.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/SeqIO.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/sam_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/alignment.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/parallel_launcher.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/copy_files.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/check_test_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/compress_all.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/correction_iteration_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/support.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/preprocess_reads_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/error_correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/pipeline.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/terminating_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/scaffold_correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/check_test_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_iteration_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/before_start_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-convert-bin-to-fasta -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gbuilder -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gmapper -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gsimplifier -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-kmercount -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-read-filter -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-kmer-estimating -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gfa-split -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/README.md -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/LICENSE -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/GPLv2.txt make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' # Use Debian-packaged yaml module find debian/spades \ -type f \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + mkdir -p debian/spades/usr/libexec/spades/ mv debian/spades/usr/bin/* debian/spades/usr/libexec/spades/ rm -f debian/spades/usr/share/spades/*.html rm -f debian/spades/usr/share/spades/manual.md rm -f debian/spades/usr/share/spades/GPLv2.txt rm -f debian/spades/usr/share/spades/README.md rm -f debian/spades/usr/share/spades/LICENSE make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_install -O--sourcedirectory=src -O--buildsystem=cmake dh_installdocs -O--sourcedirectory=src -O--buildsystem=cmake dh_installchangelogs -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' mkdir -p /build/reproducible-path/spades-4.0.0+dfsg1/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.adoc cp /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.? /build/reproducible-path/spades-4.0.0+dfsg1/debian/man dh_installman make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_python3 -O--sourcedirectory=src -O--buildsystem=cmake dh_installsystemduser -O--sourcedirectory=src -O--buildsystem=cmake dh_lintian -O--sourcedirectory=src -O--buildsystem=cmake dh_perl -O--sourcedirectory=src -O--buildsystem=cmake dh_link -O--sourcedirectory=src -O--buildsystem=cmake dh_strip_nondeterminism -O--sourcedirectory=src -O--buildsystem=cmake dh_compress -O--sourcedirectory=src -O--buildsystem=cmake dh_fixperms -O--sourcedirectory=src -O--buildsystem=cmake dh_missing -O--sourcedirectory=src -O--buildsystem=cmake dh_dwz -a -O--sourcedirectory=src -O--buildsystem=cmake dh_strip -a -O--sourcedirectory=src -O--buildsystem=cmake dh_makeshlibs -a -O--sourcedirectory=src -O--buildsystem=cmake dh_shlibdeps -a -O--sourcedirectory=src -O--buildsystem=cmake dh_installdeb -O--sourcedirectory=src -O--buildsystem=cmake dh_gencontrol -O--sourcedirectory=src -O--buildsystem=cmake dh_md5sums -O--sourcedirectory=src -O--buildsystem=cmake dh_builddeb -O--sourcedirectory=src -O--buildsystem=cmake dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_4.0.0+dfsg1-1_amd64.deb'. dpkg-deb: building package 'spades' in '../spades_4.0.0+dfsg1-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../spades_4.0.0+dfsg1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../spades_4.0.0+dfsg1-1_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: including full 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/3850233 and its subdirectories I: Current time: Mon Dec 29 19:27:10 -12 2025 I: pbuilder-time-stamp: 1767079630 Wed Nov 27 01:04:14 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Wed Nov 27 01:04:14 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Wed Nov 27 02:27:44 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Wed Nov 27 02:27:45 UTC 2024 I: spades_4.0.0+dfsg1-1_amd64.changes: Format: 1.8 Date: Wed, 02 Oct 2024 08:56:41 +0200 Source: spades Binary: spades spades-dbgsym Architecture: amd64 Version: 4.0.0+dfsg1-1 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (4.0.0+dfsg1-1) experimental; urgency=medium . * Team upload * New upstream version 4.0.0+dfsg1 * Refreshing patches * Raising Standards version to 4.7.0 (no change) * Rewriting d/copyright * Changing the paths of the files to remove when repacking * Updating the list of files to exclude when repacking * Updating files related to shipped doc in the debian/ directory * Removing the now useless override of dh_installchangelogs * Using bamtools, googletest, spoa, boost, cuckoo, joblib and xxhash from the Debian packages instead of embedded copies, updating d/control accordingly * Updating paths in d/rules * Adding missing files to the CMakeLists.txt file of the samtools part * Deactivating build-time tests of which test data have vanished from the source package * Updating homepage URI * Removing obsolete Lintian override for source-is-missing * Adding a Lintian override for the embedded (modified) copy of Zlib Checksums-Sha1: abc51686cc1edd05155d34cddacfcc7b4a643fce 169990244 spades-dbgsym_4.0.0+dfsg1-1_amd64.deb 0795493869a536f215f5c1dc20acce9f84ab39d9 11443 spades_4.0.0+dfsg1-1_amd64.buildinfo bd4a1dfd21cde67a7ab7ede3450da0fba9f2195f 8060348 spades_4.0.0+dfsg1-1_amd64.deb Checksums-Sha256: 540ae092d37508ab6cbcea3b201d268eeb7bd7457e04940938effd7b0298f740 169990244 spades-dbgsym_4.0.0+dfsg1-1_amd64.deb 409a052857951c2a85b2fe9b9e80798c35d769bad9aff0d0853619cad1525652 11443 spades_4.0.0+dfsg1-1_amd64.buildinfo 5ee8806840a5af895803b021fa991ccca82b1b22cad04b32d07f702668df07b8 8060348 spades_4.0.0+dfsg1-1_amd64.deb Files: 65a79a2268f9d91da52cf200a34fa3d9 169990244 debug optional spades-dbgsym_4.0.0+dfsg1-1_amd64.deb 1215d94e8a800f9af103c35d152d1aee 11443 science optional spades_4.0.0+dfsg1-1_amd64.buildinfo 21f1650d52c7836ee16cfb79430a2261 8060348 science optional spades_4.0.0+dfsg1-1_amd64.deb Wed Nov 27 02:27:46 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_8-40645.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1zOzKOYZ/spades_4.0.0+dfsg1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1zOzKOYZ/spades_4.0.0+dfsg1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1zOzKOYZ/spades_4.0.0+dfsg1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1zOzKOYZ/b1/spades_4.0.0+dfsg1-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.1zOzKOYZ/b2/spades_4.0.0+dfsg1-1_amd64.changes ## close_archive (total time: 0.001s) 0.001s 40 calls diffoscope.comparators.xz.XzContainer 0.000s 28 calls diffoscope.comparators.deb.DebTarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer ## command (total time: 4260.338s) 1910.142s 7628 calls readelf 1673.178s 855 calls diff 611.753s 1628 calls objdump 40.247s 24 calls objcopy 20.444s 40 calls xz 4.164s 165 calls strings 0.203s 15 calls cmp 0.203s 15 calls cmp (external) 0.004s 57 calls cmp (internal) ## compare_files (cumulative) (total time: 44152.622s) 7635.882s 1 call abc.DotChangesFile 7635.812s 2 calls abc.DebFile 7634.990s 4 calls abc.XzFile 7632.553s 2 calls abc.DebDataTarFile 7629.573s 15 calls abc.ElfFile 5967.749s 74 calls diffoscope.comparators.elf.ElfCodeSection 15.113s 260 calls diffoscope.comparators.elf.ElfSection 0.694s 12 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.150s 6 calls diffoscope.comparators.elf.ElfStringSection 0.077s 2 calls abc.TarFile 0.014s 1 call abc.TextFile 0.013s 2 calls abc.Md5sumsFile ## container_extract (total time: 31.776s) 20.447s 40 calls diffoscope.comparators.xz.XzContainer 9.881s 258 calls diffoscope.comparators.deb.DebTarContainer 1.440s 44 calls diffoscope.comparators.deb.DebContainer 0.009s 20 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 1.165s) 1.165s 52 calls linediff ## has_same_content_as (total time: 0.215s) 0.191s 15 calls abc.ElfFile 0.017s 2 calls abc.DebDataTarFile 0.002s 26 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.002s 260 calls diffoscope.comparators.elf.ElfSection 0.001s 6 calls abc.TextFile 0.001s 74 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.DebFile 0.000s 1 call abc.DotChangesFile 0.000s 12 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 6 calls diffoscope.comparators.elf.ElfStringSection ## main (total time: 7639.393s) 7639.391s 2 calls outputs 0.002s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 40 calls diffoscope.comparators.xz.XzContainer 0.000s 28 calls diffoscope.comparators.deb.DebTarContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## output (total time: 1.625s) 1.622s 1 call html 0.002s 1 call text 0.001s 1 call json ## recognizes (total time: 30.547s) 18.342s 1000 calls diffoscope.comparators.utils.archive.ArchiveMember 10.534s 4516 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 1.549s 12 calls diffoscope.comparators.binary.FilesystemFile 0.121s 216 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.400s) 0.400s 414 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 2h 7min 19.744s CPU time consumed: 2h 16min 44.566s Wed Nov 27 04:35:06 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Wed Nov 27 04:35:06 UTC 2024 E: spades failed to build reproducibly in experimental on amd64. Wed Nov 27 04:35:08 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Nov 27 04:35:08 UTC 2024 I: Submitting 16K b1/spades_4.0.0+dfsg1-1_amd64.buildinfo.asc Wed Nov 27 04:35:09 UTC 2024 I: Submitting 16K b2/spades_4.0.0+dfsg1-1_amd64.buildinfo.asc Wed Nov 27 04:35:10 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Nov 27 04:35:10 UTC 2024 I: Done submitting .buildinfo files. Wed Nov 27 04:35:10 UTC 2024 I: Removing signed spades_4.0.0+dfsg1-1_amd64.buildinfo.asc files: removed './b1/spades_4.0.0+dfsg1-1_amd64.buildinfo.asc' removed './b2/spades_4.0.0+dfsg1-1_amd64.buildinfo.asc'