Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/salmon/salmon_1.4.0+ds1-1+b4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/salmon-1.4.0+ds1-1+b4jcxk2x9g/salmon_1.4.0+ds1-1+b4_amd64.buildinfo Get source package info: salmon=1.4.0+ds1-1 Source URL: http://snapshot.notset.fr/mr/package/salmon/1.4.0+ds1-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11.1 base-passwd=3.5.50 bash=5.1-3 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 cmake=3.18.4-2 cmake-data=3.18.4-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.76 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 docutils-common=0.16+dfsg-4 docutils-doc=0.16+dfsg-4 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 fonts-font-awesome=5.0.10+really4.7.0~dfsg-4.1 fonts-lato=2.0-2.1 fonts-mathjax=2.7.9+dfsg-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 help2man=1.48.3 hostname=3.23 icu-devtools=67.1-6 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-7 libboost-atomic1.74-dev=1.74.0-9 libboost-atomic1.74.0=1.74.0-9 libboost-chrono1.74-dev=1.74.0-9 libboost-chrono1.74.0=1.74.0-9 libboost-date-time1.74-dev=1.74.0-9 libboost-date-time1.74.0=1.74.0-9 libboost-filesystem-dev=1.74.0.3 libboost-filesystem1.74-dev=1.74.0-9 libboost-filesystem1.74.0=1.74.0-9 libboost-iostreams-dev=1.74.0.3 libboost-iostreams1.74-dev=1.74.0-9 libboost-iostreams1.74.0=1.74.0-9 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-9 libboost-program-options1.74.0=1.74.0-9 libboost-regex1.74-dev=1.74.0-9 libboost-regex1.74.0=1.74.0-9 libboost-serialization1.74-dev=1.74.0-9 libboost-serialization1.74.0=1.74.0-9 libboost-system-dev=1.74.0.3 libboost-system1.74-dev=1.74.0-9 libboost-system1.74.0=1.74.0-9 libboost-thread-dev=1.74.0.3 libboost-thread1.74-dev=1.74.0-9 libboost-thread1.74.0=1.74.0-9 libboost-timer-dev=1.74.0.3 libboost-timer1.74-dev=1.74.0-9 libboost-timer1.74.0=1.74.0-9 libboost1.74-dev=1.74.0-9 libbrotli1=1.0.9-2+b2 libbwa-dev=0.7.17-6+b1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-12 libc-dev-bin=2.31-12 libc6=2.31-12 libc6-dev=2.31-12 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcereal-dev=1.3.0+dfsg-1 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.18-4 libcrypt1=1:4.4.18-4 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl3-gnutls=7.74.0-1.2 libcurl4=7.74.0-1.2 libcurl4-gnutls-dev=7.74.0-1.2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.259 libdebhelper-perl=13.3.4 libdivsufsort-dev=2.0.1-5 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.9 libeigen3-dev=3.3.9-2 libelf1=0.183-3 libexpat1=2.2.10-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libfmt-dev=7.1.3+ds1-5 libfmt7=7.1.3+ds1-5 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-6 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgff-dev=2.0.0-1 libglib2.0-0=2.66.8-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.1-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-5 libhogweed6=3.7.2-3 libhtscodecs-dev=0.5-3 libhtscodecs2=0.5-3 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libjellyfish-2.0-2=2.3.0-10 libjellyfish-2.0-dev=2.3.0-10 libjemalloc-dev=5.2.1-3 libjemalloc2=5.2.1-3 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-mathjax=2.7.9+dfsg-1 libjs-sphinxdoc=3.4.3-2 libjs-underscore=1.9.1~dfsg-3 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-5 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-5 libkrb5support0=1.18.3-5 libldap-2.4-2=2.4.57+dfsg-3 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7.2-3 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-7 libpam-modules-bin=1.4.0-7 libpam-runtime=1.4.0-7 libpam0g=1.4.0-7 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-4 libpipeline1=1.5.3-1 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 libreadline8=8.1-2 librhash0=1.4.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsmartcols1=2.36.1-7 libsparsehash-dev=2.0.3-2 libspdlog-dev=1:1.8.1+ds-2.1 libspdlog1=1:1.8.1+ds-2.1 libsqlite3-0=3.34.1-3 libssh2-1=1.9.0-3 libssl1.1=1.1.1k-1 libstaden-read-dev=1.14.13-4 libstaden-read14=1.14.13-4 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-5 libtasn1-6=4.16.0-2 libtbb-dev=2020.3-1 libtbb2=2020.3-1 libtclap-dev=1.2.4-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-5 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libuv1=1.40.0-1 libxml2=2.9.10+dfsg-6.7 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.40-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1k-1 patch=2.7.6-7 perl=5.32.1-4 perl-base=5.32.1-4 perl-modules-5.32=5.32.1-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 python-babel-localedata=2.8.0+dfsg.1-7 python-requests-doc=2.25.1+dfsg-2 python3=3.9.2-3 python3-alabaster=0.7.8-1.1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-distutils=3.9.2-1 python3-doc=3.9.2-3 python3-docutils=0.16+dfsg-4 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=2.11.3-1 python3-lib2to3=3.9.2-1 python3-markupsafe=1.1.1-1+b3 python3-minimal=3.9.2-3 python3-packaging=20.9-2 python3-pkg-resources=52.0.0-3 python3-pygments=2.7.1+dfsg-2 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-six=1.16.0-1 python3-snowballstemmer=2.1.0-1 python3-sphinx=3.4.3-2 python3-sphinx-rtd-theme=0.5.1+dfsg-1 python3-tz=2021.1-1 python3-urllib3=1.26.4-1 python3.9=3.9.2-1 python3.9-doc=3.9.2-1 python3.9-minimal=3.9.2-1 rapidjson-dev=1.1.0+dfsg2-7 rapmap-dev=0.15.0+dfsg-1 readline-common=8.1-2 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sphinx-common=3.4.3-2 sphinx-doc=3.4.3-2 sphinx-rtd-theme-common=0.5.1+dfsg-1 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-7 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210607T084757Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d salmon=1.4.0+ds1-1 && mkdir -p /build/salmon-KbMTx0 && dpkg-source --no-check -x /*.dsc /build/salmon-KbMTx0/salmon-1.4.0+ds1 && cd /build/salmon-KbMTx0/salmon-1.4.0+ds1 && { printf '%s' 'salmon (1.4.0+ds1-1+b4) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 03 Jun 2021 01:05:41 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/salmon-KbMTx0" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/salmon-KbMTx0/salmon-1.4.0+ds1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1622682341" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/salmon-KbMTx0 /tmp/salmon-1.4.0+ds1-1+b4jcxk2x9g bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210607T084757Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.jVLQClmKJK as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.jVLQClmKJK Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210607T084757Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210607T084757Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (799 kB/s) Selecting previously unselected package libfakeroot: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 ... 4667 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-12) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210607T084757Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.jVLQClmKJK Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210607T084757Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1158 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.jVLQClmKJK I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d salmon=1.4.0+ds1-1 && mkdir -p /build/salmon-KbMTx0 && dpkg-source --no-check -x /*.dsc /build/salmon-KbMTx0/salmon-1.4.0+ds1 && cd /build/salmon-KbMTx0/salmon-1.4.0+ds1 && { printf '%s' 'salmon (1.4.0+ds1-1+b4) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 03 Jun 2021 01:05:41 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/salmon-KbMTx0"' exec /tmp/mmdebstrap.jVLQClmKJK Reading package lists... NOTICE: 'salmon' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/salmon.git Please use: git clone https://salsa.debian.org/med-team/salmon.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6588 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main salmon 1.4.0+ds1-1 (dsc) [2518 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main salmon 1.4.0+ds1-1 (tar) [5609 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main salmon 1.4.0+ds1-1 (diff) [976 kB] Fetched 6588 kB in 5s (1224 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'salmon_1.4.0+ds1-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting salmon in /build/salmon-KbMTx0/salmon-1.4.0+ds1 dpkg-source: info: unpacking salmon_1.4.0+ds1.orig.tar.xz dpkg-source: info: unpacking salmon_1.4.0+ds1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying pufferfish dpkg-source: info: applying disable-version-check.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/salmon-KbMTx0/salmon-1.4.0+ds1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1622682341" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.jVLQClmKJK dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.4.0+ds1-1+b4 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' dh_auto_clean rm -rf external rm -f debian/*.1 rm -Rf sample_data cd doc && /usr/bin/make clean make[2]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/doc' rm -rf build/* make[2]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/doc' rm -rf tests/unitTests make[1]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' dh_clean debian/rules binary-arch dh binary-arch --with sphinxdoc dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' # See here # https://github.com/COMBINE-lab/salmon/issues/87 # for a discussion with upstream why it is necessary to include rapmap source mkdir -p /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap cp -av /usr/share/rapmap/src/* /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap '/usr/share/rapmap/src/HitManager.cpp' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/HitManager.cpp' '/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapFileSystem.cpp' '/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapSAIndex.cpp' '/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp' '/usr/share/rapmap/src/RapMapUtils.cpp' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapUtils.cpp' '/usr/share/rapmap/src/bit_array.c' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE cd obj-x86_64-linux-gnu && 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_PACKAGE_NO_PACKAGE_REGISTRY=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 -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE .. CC: gcc CC version: -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- 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 Detected non-ARM host. Setting USE_ARM to false. version: 1.4.0 -- CMAKE_BUILD_TYPE = Release -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE Building with CONDA_BUILD flag Making Release build setting -DHAVE_NUMERIC_LIMITS128 running cd "/build/salmon-KbMTx0/salmon-1.4.0+ds1" && cp -r ./debian/external ./ 2>&1 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: /usr/lib/x86_64-linux-gnu/libc.so -- Found LibLZMA: lzma (found version "5.2.5") Found liblzma library: lzma =========================================== -- Found BZip2: -lbz2 (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: -lbz2 =========================================== -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.59.0") found components: iostreams filesystem system timer chrono program_options BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = BOOST INCLUDE DIR = /usr/include BOOST INCLUDE DIRS = /usr/include BOOST LIB DIR = /usr/lib/x86_64-linux-gnu BOOST LIBRARIES = Boost::iostreams;Boost::filesystem;Boost::system;Boost::timer;Boost::chrono;Boost::program_options -- Found Cereal: /usr/include -- Cereal found (include: /usr/include) FOUND SUITABLE TBB VERSION : 2020.3 TBB_LIBRARIES = -- libgff ver. 2.0.0 found. -- include: /usr/include/ -- lib : /usr/lib/ -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") -- Found libstadenio: /usr/lib/x86_64-linux-gnu/libstaden-read.so -- Staden IOLib found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ CC: /usr/bin/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 NO_IPO = FALSE TBB_LIBRARIES = -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHED_RAPMAP -- Build files have been written to: /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/salmon-KbMTx0/salmon-1.4.0+ds1 -B/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake --color= make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake --color= make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". Scanning dependencies of target ntcard Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend.internal". Scanning dependencies of target ksw2pp_sse4 make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build Scanning dependencies of target graphdump make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build Scanning dependencies of target twopaco make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 1%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 2%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c [ 3%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp [ 4%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp [ 5%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp [ 6%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp [ 7%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/nthll.cpp [ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common/streamfastaparser.h:8, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp:18: /usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 9%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 9%] Built target ksw2pp_sse4 make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend.internal". Scanning dependencies of target ksw2pp_basic make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 10%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/kalloc.c [ 11%] Linking CXX static library libntcard.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:14, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/compat/thread:21:146: note: ‘#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ /usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o [ 12%] Built target ntcard cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". Scanning dependencies of target ksw2pp_sse2 make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/task_scheduler_init.h:21:154: note: ‘#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c [ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c [ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c [ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c [ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 18%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 19%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c [ 19%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 19%] Built target ksw2pp_sse2 [ 20%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp [ 21%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.h:8, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:4: /usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 21%] Built target ksw2pp_basic make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/depend.internal". 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Scanning dependencies of target puffer make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 22%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". 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Scanning dependencies of target salmon_core make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 23%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/jellyfish/mer_dna.cc [ 23%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/xxhash.c cc1: warning: command-line option ‘-Wno-reorder’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-Wno-deprecated-copy’ is valid for C++/ObjC++ but not for C [ 24%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/TranscriptGroup.cpp [ 25%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/EffectiveLengthStats.cpp [ 26%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/LibraryFormat.cpp [ 27%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp [ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/GenomicFeature.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::value_type = std::pair, unsigned int>]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::mapped_type = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, unsigned int> >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 29%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp [ 30%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.h:8, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:4: /usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/VersionChecker.cpp [ 32%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 33%] Linking CXX static library libgraphdump.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o /usr/bin/ranlib libgraphdump.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 33%] Built target graphdump [ 34%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:14, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/compat/thread:21:146: note: ‘#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/task_scheduler_init.h:21:154: note: ‘#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:14, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/compat/thread:21:146: note: ‘#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/task_scheduler_init.h:21:154: note: ‘#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 35%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SBModel.cpp [ 36%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/FastxParser.cpp [ 37%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp [ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp [ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/StadenUtils.cpp [ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonUtils.cpp [ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp [ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndex.cpp [ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp [ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/DistributionUtils.cpp [ 44%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp [ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 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-Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonExceptions.cpp [ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonStringUtils.cpp [ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SimplePosBias.cpp [ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SGSmooth.cpp [ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/pufferfish/metro/metrohash64.cpp make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". Scanning dependencies of target alevin_core make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 48%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/edlib.cpp [ 49%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SingleCellProtocols.cpp [ 50%] Linking CXX static library libsalmon_core.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-10" cr libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o "/usr/bin/gcc-ranlib-10" libsalmon_core.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 50%] Built target salmon_core make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu 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Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". Scanning dependencies of target ksw2pp make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 51%] Linking CXX static library libksw2pp.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-10" cr libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/gcc-ranlib-10" libksw2pp.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 51%] Built target ksw2pp [ 52%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/AlevinUtils.cpp [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/edlib.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/edlib.cpp [ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/Util.cpp [ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/rank9sel.cpp [ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/rank9b.cpp [ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishValidate.cpp [ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishStats.cpp [ 59%] Linking CXX static library libalevin_core.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-10" cr libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o "/usr/bin/gcc-ranlib-10" libalevin_core.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 59%] Built target alevin_core make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake --color= Dependee 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Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". Scanning dependencies of target unitTests make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 60%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/tests/UnitTests.cpp [ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishTestLookup.cpp [ 62%] Linking CXX static library libtwopaco.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/ranlib libtwopaco.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 62%] Built target twopaco [ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishExamine.cpp [ 64%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/FragmentLengthDistribution.cpp [ 65%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/src/pufferfish/rank9b.cpp [ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FastxParser.cpp [ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp [ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferFS.cpp [ 69%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/xxhash.c cc1: warning: command-line option ‘-Wno-reorder’ is valid for C++/ObjC++ but not for C In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::value_type = std::pair, unsigned int>]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::mapped_type = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, unsigned int> >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 70%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp [ 71%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/MemCollector.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3234:9: required from ‘std::pair::ne_iterator, bool> spp::sparse_hashtable::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparsetable::ne_iterator = spp::Two_d_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:4221:73: required from ‘std::pair::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparse_hashtable::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator = spp::Two_d_iterator, const spp::sparsegroup, spp::libc_allocator > >*, const std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:490:32: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 71%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/MemChainer.cpp [ 72%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PuffAligner.cpp [ 73%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishAligner.cpp [ 74%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = pufferfish::util::ContigBlock]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from ‘Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 75%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/src/metro/metrohash64.cpp [ 76%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/LibraryFormat.cpp [ 77%] Linking CXX executable unitTests cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -o unitTests -L/build/salmon-KbMTx0/salmon-1.4.0+ds1/lib -L/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" libalevin_core.a libsalmon_core.a -lgff /usr/lib/x86_64-linux-gnu/libstaden-read.so -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl -pthread Copying unitTests cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/unitTests /build/salmon-KbMTx0/salmon-1.4.0+ds1/tests/unitTests make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 77%] Built target unitTests [ 78%] Linking CXX static library libpuffer.a cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 /usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o /usr/bin/ranlib libpuffer.a make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 78%] Built target puffer make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-KbMTx0/salmon-1.4.0+ds1 /build/salmon-KbMTx0/salmon-1.4.0+ds1/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/DependInfo.cmake --color= Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/DependInfo.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/depend.internal". Dependee "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/depend.internal". Scanning dependencies of target salmon make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 79%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/CollapsedEMOptimizer.cpp [ 80%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o [ 81%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/CollapsedGibbsSampler.cpp cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/EMUtils.cpp [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/CollapsedCellOptimizer.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/pcg_random.hpp:104, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/CollapsedGibbsSampler.cpp:23: /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/pcg_extras.hpp:563:60: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ [ 83%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/Salmon.cpp [ 84%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/BuildSalmonIndex.cpp [ 85%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/Graph.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/Graph.cpp [ 86%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/DedupUMI.cpp [ 87%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/Alevin.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/AlevinUtils.hpp:46, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/Graph.hpp:8, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/Graph.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of ‘T* spp::libc_allocator::reallocate(spp::libc_allocator::pointer, size_t) [with T = std::pair, unsigned int>; spp::libc_allocator::pointer = std::pair, unsigned int>*; size_t = long unsigned int]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from ‘void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::pointer = std::pair, unsigned int>*; spp::sparsegroup::value_type = std::pair, unsigned int>; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsetable::reference = std::pair, unsigned int>&; spp::sparsetable::value_type = std::pair, unsigned int>; spp::sparsetable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::reference = std::pair, unsigned int>&; spp::sparse_hashtable::value_type = std::pair, unsigned int>; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::value_type = std::pair, unsigned int>]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3809:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::mapped_type = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/Graph.cpp:10:29: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair, unsigned int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/graph/graph_traits.hpp:14, from /usr/include/boost/graph/depth_first_search.hpp:17, from /usr/include/boost/graph/connected_components.hpp:15, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/Graph.hpp:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/Graph.cpp:1: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair, unsigned int>’ declared here 211 | struct pair | ^~~~ [ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/AlevinHash.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/AlevinHash.cpp [ 88%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/AlevinUtils.hpp:46, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/Graph.hpp:8, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of ‘T* spp::libc_allocator::reallocate(spp::libc_allocator::pointer, size_t) [with T = std::pair, unsigned int>; spp::libc_allocator::pointer = std::pair, unsigned int>*; size_t = long unsigned int]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from ‘void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::pointer = std::pair, unsigned int>*; spp::sparsegroup::value_type = std::pair, unsigned int>; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from ‘void spp::sparsetable::move(spp::sparsetable::size_type, spp::sparsetable::reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsetable::size_type = long unsigned int; spp::sparsetable::reference = std::pair, unsigned int>&; spp::sparsetable::value_type = std::pair, unsigned int>]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from ‘void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from ‘bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from ‘void spp::sparse_hashtable::resize(spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3795:51: required from ‘void spp::sparse_hash_map::resize(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3797:41: required from ‘void spp::sparse_hash_map::reserve(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/DedupUMI.cpp:39:36: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair, unsigned int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/graph/graph_traits.hpp:14, from /usr/include/boost/graph/depth_first_search.hpp:17, from /usr/include/boost/graph/connected_components.hpp:15, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/Graph.hpp:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, from /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair, unsigned int>’ declared here 211 | struct pair | ^~~~ [ 89%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/WhiteList.cpp In file included from /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/WhiteList.cpp:2: /usr/include/tbb/task_scheduler_init.h:21:154: note: ‘#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’ 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2883:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2883:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2899:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2899:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::InDrop; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::InDrop; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2914:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::InDrop; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::InDrop; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2914:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2929:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2929:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [ 90%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonQuantify.cpp /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2944:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2944:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/FragmentLengthDistribution.cpp /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2959:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2959:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2974:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2974:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2989:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2989:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3004:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3004:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3019:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3019:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3023:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [ 92%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/FragmentStartPositionDistribution.cpp /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from ‘sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from ‘void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3023:75: required from here /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [ 93%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/GZipWriter.cpp [ 94%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonQuantMerge.cpp [ 95%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/ProgramOptionsGenerator.cpp [ 96%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/FASTAParser.cpp [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/AlignmentModel.cpp [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/SalmonQuantifyAlignments.cpp [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/salmon-KbMTx0/salmon-1.4.0+ds1/src/BAMUtils.cpp [100%] Linking CXX executable salmon cd /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/salmon-KbMTx0/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/build/salmon-KbMTx0/salmon-1.4.0+ds1/lib -L/build/salmon-KbMTx0/salmon-1.4.0+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -ljemalloc -ltbb -ltbbmalloc -lrt -ldl -pthread make[4]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [100%] Built target salmon make[3]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' mv doc/source/license.rst doc/ # unused PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html Running Sphinx v3.4.3 making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 6 source files that are out of date updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] alevin reading sources... [ 33%] building reading sources... [ 50%] file_formats reading sources... [ 66%] index reading sources... [ 83%] library_type reading sources... [100%] salmon /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:32: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:32: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:52: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:75: WARNING: Block quote ends without a blank line; unexpected unindent. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:79: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:79: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:89: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:89: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:95: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:95: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:123: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:123: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:129: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:129: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:135: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:135: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:151: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:151: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:198: WARNING: Title underline too short. Output Quality Check ------------- /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:198: WARNING: Title underline too short. Output Quality Check ------------- /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:247: WARNING: Title underline too short. BibTex ---- /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:247: WARNING: Title underline too short. BibTex ---- /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:281: WARNING: Duplicate explicit target name: "swish". /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:281: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:283: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:285: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:287: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:289: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:291: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:293: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/alevin.rst:295: WARNING: Footnote [#] is not referenced. /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". /build/salmon-KbMTx0/salmon-1.4.0+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] alevin writing output... [ 33%] building writing output... [ 50%] file_formats writing output... [ 66%] index writing output... [ 83%] library_type writing output... [100%] salmon generating indices... genindex done writing additional pages... search done copying images... [100%] ReadLibraryIllustration.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 34 warnings. The HTML pages are in doc/build/html. mv doc/license.rst doc/source/ cd obj*/src && \ help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\ ./salmon > ../../debian/salmon.1 && \ for option in index quant swim; do help2man --no-discard-stderr \ --version-string="1.4.0+ds1" --no-info "./salmon --no-version-check ${option}" \ --include=../../debian/salmon-${option}-man-include \ > ../../debian/salmon-${option}.1; done make[1]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=-j1 make[2]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j1 Test project /build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu Start 1: unit_tests 1/2 Test #1: unit_tests ....................... Passed 0.75 sec Start 2: salmon_read_test_quasi 2/2 Test #2: salmon_read_test_quasi ........... Passed 1.64 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 2.40 sec make[2]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' dh_auto_install cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/salmon-KbMTx0/salmon-1.4.0\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/salmon-KbMTx0/salmon-1.4.0+ds1 -B/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libntcard.a -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libgraphdump.a -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libtwopaco.a -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/bin/salmon -- Installing: /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libsalmon_core.a Installation complete. Please ensure the following paths are set properly. ========================================================================== Please add /usr/bin to your PATH Please add /usr/lib to your LD_LIBRARY_PATH ========================================================================== make[2]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' rm -Rvf /build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' removed directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libgraphdump.a' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libtwopaco.a' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libsalmon_core.a' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' removed directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' removed directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard' removed '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib/libntcard.a' removed directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1/debian/salmon/usr/lib' make[1]: Leaving directory '/build/salmon-KbMTx0/salmon-1.4.0+ds1' dh_installdocs -a dh_sphinxdoc -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.4.0+ds1-1+b4_amd64.deb'. dpkg-deb: building package 'salmon' in '../salmon_1.4.0+ds1-1+b4_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../salmon_1.4.0+ds1-1+b4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/salmon-KbMTx0 /tmp/salmon-1.4.0+ds1-1+b4jcxk2x9g I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.jVLQClmKJK... I: success in 3661.8740 seconds md5: salmon-dbgsym_1.4.0+ds1-1+b4_amd64.deb: OK md5: salmon_1.4.0+ds1-1+b4_amd64.deb: OK sha1: salmon-dbgsym_1.4.0+ds1-1+b4_amd64.deb: OK sha1: salmon_1.4.0+ds1-1+b4_amd64.deb: OK sha256: salmon-dbgsym_1.4.0+ds1-1+b4_amd64.deb: OK sha256: salmon_1.4.0+ds1-1+b4_amd64.deb: OK Checksums: OK