Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/shasta/shasta_0.8.0-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/shasta-0.8.0-2m1k3xm5w/shasta_0.8.0-2_all.buildinfo Get source package info: shasta=0.8.0-2 Source URL: http://snapshot.notset.fr/mr/package/shasta/0.8.0-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5+b1 binutils=2.37-10.1 binutils-common=2.37-10.1 binutils-x86-64-linux-gnu=2.37-10.1 bsdextrautils=2.37.2-5 bsdutils=1:2.37.2-5 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 chrpath=0.16-2+b1 cmake=3.22.1-1+b1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-13 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-exec=0.23.4 dh-python=5.20220101 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-13 gcc=4:11.2.0-2 gcc-11=11.2.0-13 gcc-11-base=11.2.0-13 gettext=0.21-4 gettext-base=0.21-4 gfortran=4:11.2.0-2 gfortran-11=11.2.0-13 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 ibverbs-providers=38.0-1 icu-devtools=67.1-7 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.5.2-1 libasan6=11.2.0-13 libatomic1=11.2.0-13 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10.1 libblas-dev=3.10.0-2 libblas3=3.10.0-2 libblkid1=2.37.2-5 libboost-all-dev=1.74.0.3 libboost-atomic-dev=1.74.0.3 libboost-atomic1.74-dev=1.74.0-13 libboost-atomic1.74.0=1.74.0-13 libboost-chrono-dev=1.74.0.3 libboost-chrono1.74-dev=1.74.0-13 libboost-chrono1.74.0=1.74.0-13 libboost-container-dev=1.74.0.3 libboost-container1.74-dev=1.74.0-13 libboost-container1.74.0=1.74.0-13 libboost-context-dev=1.74.0.3 libboost-context1.74-dev=1.74.0-13 libboost-context1.74.0=1.74.0-13 libboost-coroutine-dev=1.74.0.3 libboost-coroutine1.74-dev=1.74.0-13 libboost-coroutine1.74.0=1.74.0-13 libboost-date-time-dev=1.74.0.3 libboost-date-time1.74-dev=1.74.0-13 libboost-date-time1.74.0=1.74.0-13 libboost-dev=1.74.0.3 libboost-exception-dev=1.74.0.3 libboost-exception1.74-dev=1.74.0-13 libboost-fiber-dev=1.74.0.3 libboost-fiber1.74-dev=1.74.0-13 libboost-fiber1.74.0=1.74.0-13 libboost-filesystem-dev=1.74.0.3 libboost-filesystem1.74-dev=1.74.0-13 libboost-filesystem1.74.0=1.74.0-13 libboost-graph-dev=1.74.0.3 libboost-graph-parallel-dev=1.74.0.3 libboost-graph-parallel1.74-dev=1.74.0-13 libboost-graph-parallel1.74.0=1.74.0-13 libboost-graph1.74-dev=1.74.0-13 libboost-graph1.74.0=1.74.0-13 libboost-iostreams-dev=1.74.0.3 libboost-iostreams1.74-dev=1.74.0-13 libboost-iostreams1.74.0=1.74.0-13 libboost-locale-dev=1.74.0.3 libboost-locale1.74-dev=1.74.0-13 libboost-locale1.74.0=1.74.0-13 libboost-log-dev=1.74.0.3 libboost-log1.74-dev=1.74.0-13 libboost-log1.74.0=1.74.0-13 libboost-math-dev=1.74.0.3 libboost-math1.74-dev=1.74.0-13 libboost-math1.74.0=1.74.0-13 libboost-mpi-dev=1.74.0.3 libboost-mpi-python-dev=1.74.0.3 libboost-mpi-python1.74-dev=1.74.0-13 libboost-mpi-python1.74.0=1.74.0-13 libboost-mpi1.74-dev=1.74.0-13 libboost-mpi1.74.0=1.74.0-13 libboost-nowide-dev=1.74.0.3 libboost-nowide1.74-dev=1.74.0-13 libboost-nowide1.74.0=1.74.0-13 libboost-numpy-dev=1.74.0.3 libboost-numpy1.74-dev=1.74.0-13 libboost-numpy1.74.0=1.74.0-13 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-13 libboost-program-options1.74.0=1.74.0-13 libboost-python-dev=1.74.0.3 libboost-python1.74-dev=1.74.0-13 libboost-python1.74.0=1.74.0-13 libboost-random-dev=1.74.0.3 libboost-random1.74-dev=1.74.0-13 libboost-random1.74.0=1.74.0-13 libboost-regex-dev=1.74.0.3 libboost-regex1.74-dev=1.74.0-13 libboost-regex1.74.0=1.74.0-13 libboost-serialization-dev=1.74.0.3 libboost-serialization1.74-dev=1.74.0-13 libboost-serialization1.74.0=1.74.0-13 libboost-stacktrace-dev=1.74.0.3 libboost-stacktrace1.74-dev=1.74.0-13 libboost-stacktrace1.74.0=1.74.0-13 libboost-system-dev=1.74.0.3 libboost-system1.74-dev=1.74.0-13 libboost-system1.74.0=1.74.0-13 libboost-test-dev=1.74.0.3 libboost-test1.74-dev=1.74.0-13 libboost-test1.74.0=1.74.0-13 libboost-thread-dev=1.74.0.3 libboost-thread1.74-dev=1.74.0-13 libboost-thread1.74.0=1.74.0-13 libboost-timer-dev=1.74.0.3 libboost-timer1.74-dev=1.74.0-13 libboost-timer1.74.0=1.74.0-13 libboost-tools-dev=1.74.0.3 libboost-type-erasure-dev=1.74.0.3 libboost-type-erasure1.74-dev=1.74.0-13 libboost-type-erasure1.74.0=1.74.0-13 libboost-wave-dev=1.74.0.3 libboost-wave1.74-dev=1.74.0-13 libboost-wave1.74.0=1.74.0-13 libboost1.74-dev=1.74.0-13 libboost1.74-tools-dev=1.74.0-13 libbrotli1=1.0.9-2+b3 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-1 libc-dev-bin=2.33-1 libc6=2.33-1 libc6-dev=2.33-1 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcbor0.8=0.8.0-2 libcc1-0=11.2.0-13 libcereal-dev=1.3.0+dfsg-2 libcom-err2=1.46.5-1 libcpu-features-dev=0.6.0-3 libcrypt-dev=1:4.4.27-1 libcrypt1=1:4.4.27-1 libctf-nobfd0=2.37-10.1 libctf0=2.37-10.1 libcurl3-gnutls=7.80.0-3 libcurl4=7.80.0-3 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.1 libedit2=3.1-20210910-1 libelf1=0.186-1 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.4.2-1 libexpat1-dev=2.4.2-1 libfabric1=1.11.0-3 libffi8=3.4.2-3 libfido2-1=1.9.0-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-13 libgcc-s1=11.2.0-13 libgcrypt20=1.9.4-5 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran-11-dev=11.2.0-13 libgfortran5=11.2.0-13 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-4 libgomp1=11.2.0-13 libgpg-error0=1.43-1 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhwloc-dev=2.7.0-1 libhwloc-plugins=2.7.0-1 libhwloc15=2.7.0-1 libibverbs-dev=38.0-1 libibverbs1=38.0-1 libicu-dev=67.1-7 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-13 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.13.0+dfsg-1 libjs-sphinxdoc=4.3.2-1 libjs-underscore=1.9.1~dfsg-4 libjsoncpp25=1.9.5-2 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack-dev=3.10.0-2 liblapack3=3.10.0-2 libldap-2.4-2=2.4.59+dfsg-1 liblmdb0=0.9.24-1 liblsan0=11.2.0-13 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmbedcrypto3=2.16.11-0.3 libmbedtls12=2.16.11-0.3 libmbedx509-0=2.16.11-0.3 libmd0=1.0.4-1 libmount1=2.37.2-5 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.2-1 libopenmpi3=4.1.2-1 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpciaccess0=0.16-1 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-2 libpmix-dev=4.1.1~rc6-1 libpmix2=4.1.1~rc6-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.9=3.9.9-2 libpython3.9-dev=3.9.9-2 libpython3.9-minimal=3.9.9-2 libpython3.9-stdlib=3.9.9-2 libquadmath0=11.2.0-13 librdmacm1=38.0-1 libreadline8=8.1-2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsepol2=3.3-1 libseqan2-dev=2.4.0+dfsg-14 libsigsegv2=2.13-1 libsmartcols1=2.37.2-5 libspoa-dev=4.0.7+ds-2 libspoa7.0.0=4.0.7+ds-2 libsqlite3-0=3.37.1-1 libssh2-1=1.10.0-2 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-13 libstdc++6=11.2.0-13 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-13 libubsan1=11.2.0-13 libuchardet0=0.0.7-1 libucx0=1.12.0-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-5 libuv1=1.42.0-1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.12+dfsg-5+b1 libxnvctrl0=470.82.00-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-2 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-4 mawk=1.3.4.20200120-2 media-types=4.0.0 mpi-default-bin=1.14 mpi-default-dev=1.14 ncbi-blast+=2.12.0+ds-2 ncbi-data=6.1.20170106+dfsg1-9 ncurses-base=6.3-1 ncurses-bin=6.3-1 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.2-1 openmpi-common=4.1.2-1 openssh-client=1:8.7p1-4 openssl=1.1.1m-1 passwd=1:4.8.1-2 patch=2.7.6-7 patchelf=0.14.3-1 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 pybind11-dev=2.8.1-3 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.9.8-1 python3-alabaster=0.7.12-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-dev=3.9.8-1 python3-distutils=3.9.9-3 python3-docutils=0.17.1+dfsg-2 python3-idna=3.2-2 python3-imagesize=1.3.0-1 python3-jinja2=3.0.1-2 python3-lib2to3=3.9.9-3 python3-markupsafe=2.0.1-2+b1 python3-minimal=3.9.8-1 python3-packaging=21.3-1 python3-pkg-resources=59.6.0-1 python3-pybind11=2.8.1-3 python3-pygments=2.10.0+dfsg-1 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=3.3-1 python3-six=1.16.0-3 python3-snowballstemmer=2.2.0-1 python3-sphinx=4.3.2-1 python3-tz=2021.3-1 python3-urllib3=1.26.5-1~exp1 python3.9=3.9.9-2 python3.9-dev=3.9.9-2 python3.9-minimal=3.9.9-2 rapidjson-dev=1.1.0+dfsg2-7 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.3.2-1 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-5 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/20220109T025204Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220109T025204Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220103T215446Z/ 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 shasta=0.8.0-2 && mkdir -p /build/shasta-McdAxI && dpkg-source --no-check -x /*.dsc /build/shasta-McdAxI/shasta-0.8.0 && chown -R builduser:builduser /build/shasta-McdAxI" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/shasta-McdAxI/shasta-0.8.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1641238816" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/shasta-McdAxI /tmp/shasta-0.8.0-2m1k3xm5w bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220103T215446Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.pZztlBqNcQ 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.pZztlBqNcQ Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-5). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220103T215446Z unstable/main amd64 libfakeroot amd64 1.26-1.1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220103T215446Z unstable/main amd64 fakeroot amd64 1.26-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (983 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 ... 4684 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1.1_amd64.deb ... Unpacking fakeroot (1.26-1.1) ... Setting up libfakeroot:amd64 (1.26-1.1) ... Setting up fakeroot (1.26-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-1) ... 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/20220109T025204Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220109T025204Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220103T215446Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.pZztlBqNcQ Get:1 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm InRelease [129 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220103T215446Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main amd64 Packages [11.1 MB] Fetched 23.0 MB in 19s (1205 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.pZztlBqNcQ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d shasta=0.8.0-2 && mkdir -p /build/shasta-McdAxI && dpkg-source --no-check -x /*.dsc /build/shasta-McdAxI/shasta-0.8.0 && chown -R builduser:builduser /build/shasta-McdAxI"' exec /tmp/mmdebstrap.pZztlBqNcQ Reading package lists... NOTICE: 'shasta' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/shasta.git Please use: git clone https://salsa.debian.org/med-team/shasta.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3811 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main shasta 0.8.0-2 (dsc) [2369 B] Get:2 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main shasta 0.8.0-2 (tar) [3796 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220109T025204Z bookworm/main shasta 0.8.0-2 (diff) [11.7 kB] Fetched 3811 kB in 3s (1238 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'shasta_0.8.0-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting shasta in /build/shasta-McdAxI/shasta-0.8.0 dpkg-source: info: unpacking shasta_0.8.0.orig.tar.gz dpkg-source: info: unpacking shasta_0.8.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying libspoa7.0.0 dpkg-source: info: applying modify_cmakelists.patch dpkg-source: info: applying fix-build-with-pybind11.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/shasta-McdAxI/shasta-0.8.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1641238816" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.pZztlBqNcQ dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.8.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary-indep dh binary-indep --with python3,sphinxdoc dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0' dh_auto_configure -- -DBUILD_ID=0.8.0 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_USE_PACKAGE_REGISTRY=OFF -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 -DBUILD_ID=0.8.0 .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is x86_64 -- CMAKE_SYSTEM_NAME is Linux -- MACOS is OFF -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_APPIMAGE is OFF -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.8.0 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/shasta-McdAxI/shasta-0.8.0 -B/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/CMakeFiles /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/shasta-McdAxI/shasta-0.8.0 /build/shasta-McdAxI/shasta-0.8.0/staticLibrary /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/shasta-McdAxI/shasta-0.8.0 /build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' [ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Alignment.cpp [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Align4.cpp [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssembledSegment.cpp cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AlignmentGraph.cpp [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Align4.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssembledSegment.cpp cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Assembler.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o [ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign.cpp cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AlignmentGraph.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Alignment.cpp [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign1.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Assembler.cpp [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c 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/build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign.cpp [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign4.cpp [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign1.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign3.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlign4.cpp [ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c 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-ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerAlignments.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 22%] Building CXX object 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerHttpServer.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerLowHash.cpp [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerConnectivityGraph.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraph.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 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-O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphForks.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphForks.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphForks.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphForks.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphForks.cpp /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp: In member function ‘void shasta::Assembler::cleanupDuplicateMarkersPattern2(shasta::MarkerGraph::VertexId, uint64_t, uint64_t, bool, std::vector >&, std::vector&, bool, std::ostream&)’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp:463:40: warning: loop variable ‘markerDescriptor’ creates a copy from type ‘const MarkerDescriptor’ {aka ‘const std::pair’} [-Wrange-loop-construct] 463 | for(const MarkerDescriptor markerDescriptor: componentDescriptors) { | ^~~~~~~~~~~~~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp:463:40: note: use reference type to prevent copying 463 | for(const MarkerDescriptor markerDescriptor: componentDescriptors) { | ^~~~~~~~~~~~~~~~ | & [ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphRefine.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphRefine.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphRefine.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphRefine.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphRefine.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerHttpServer-MarkerGraph.cpp [ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerHttpServer-ReadGraph.cpp [ 33%] Building CXX object 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Forks.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Forks.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Forks.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Forks.cpp [ 42%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Histogram.cpp [ 42%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/HttpServer.cpp [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/InducedAlignment.cpp In file included from /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:2: In copy constructor ‘shasta::AssemblyGraph2Edge::Branch::Branch(const shasta::AssemblyGraph2Edge::Branch&)’, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Args = {const shasta::AssemblyGraph2Edge::Branch&}]’ at /usr/include/c++/11/bits/stl_construct.h:119:7, inlined from ‘static _ForwardIterator std::__uninitialized_fill_n<_TrivialValueType>::__uninit_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = shasta::AssemblyGraph2Edge::Branch*; _Size = long unsigned int; _Tp = shasta::AssemblyGraph2Edge::Branch; bool _TrivialValueType = false]’ at /usr/include/c++/11/bits/stl_uninitialized.h:237:18, inlined from ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = shasta::AssemblyGraph2Edge::Branch*; _Size = long unsigned int; _Tp = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/bits/stl_uninitialized.h:297:17, inlined from ‘_ForwardIterator std::__uninitialized_fill_n_a(_ForwardIterator, _Size, const _Tp&, std::allocator<_Tp2>&) [with _ForwardIterator = shasta::AssemblyGraph2Edge::Branch*; _Size = long unsigned int; _Tp = shasta::AssemblyGraph2Edge::Branch; _Tp2 = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/bits/stl_uninitialized.h:410:39, inlined from ‘void std::vector<_Tp, _Alloc>::_M_fill_initialize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/stl_vector.h:1596:33, inlined from ‘std::vector<_Tp, _Alloc>::vector(std::vector<_Tp, _Alloc>::size_type, const value_type&, const allocator_type&) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/stl_vector.h:525:27, inlined from ‘shasta::AssemblyGraph2Edge::AssemblyGraph2Edge(uint64_t, const MarkerGraphPath&, bool)’ at /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:142:17, inlined from ‘boost::adjacency_list::edge_descriptor shasta::AssemblyGraph2::addEdge(const MarkerGraphPath&, bool)’ at /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:497:9: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:90:11: warning: ‘*(const __vector(2) long unsigned int*)((char*)& + offsetof(shasta::AssemblyGraph2Edge::Branch, shasta::AssemblyGraph2Edge::Branch::minimumCoverage))’ may be used uninitialized [-Wmaybe-uninitialized] 90 | class Branch { | ^~~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp: In member function ‘boost::adjacency_list::edge_descriptor shasta::AssemblyGraph2::addEdge(const MarkerGraphPath&, bool)’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:142:64: note: ‘’ declared here 142 | id(id), branches(1, Branch(path, containsSecondaryEdges)) {} | ^ [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalAlignmentCandidateGraph.cpp [ 44%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalAlignmentGraph.cpp [ 44%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalAssemblyGraph.cpp [ 45%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalMarkerGraph-Write.cpp In constructor ‘shasta::AssemblyGraph2Edge::Branch::Branch(shasta::AssemblyGraph2Edge::Branch&&)’, inlined from ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = shasta::AssemblyGraph2Edge::Branch; _Args = {shasta::AssemblyGraph2Edge::Branch}; _Tp = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/ext/new_allocator.h:162:4, inlined from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = shasta::AssemblyGraph2Edge::Branch; _Args = {shasta::AssemblyGraph2Edge::Branch}; _Tp = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/bits/alloc_traits.h:516:17, inlined from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {shasta::AssemblyGraph2Edge::Branch}; _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/vector.tcc:115:30, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/stl_vector.h:1204:21, inlined from ‘void shasta::AssemblyGraph2::handleSuperbubble0(shasta::AssemblyGraph2::Superbubble&)’ at /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:3565:35: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:90:11: warning: ‘*(__vector(2) long unsigned int*)((char*)& + offsetof(shasta::AssemblyGraph2Edge::Branch, shasta::AssemblyGraph2Edge::Branch::minimumCoverage))’ may be used uninitialized [-Wmaybe-uninitialized] 90 | class Branch { | ^~~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp: In member function ‘void shasta::AssemblyGraph2::handleSuperbubble0(shasta::AssemblyGraph2::Superbubble&)’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:3565:85: note: ‘’ declared here 3565 | newEdge.branches.push_back(E::Branch(markerGraphPath, containsSecondaryEdges)); | ^ [ 45%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalMarkerGraph.cpp [ 46%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalReadGraph.cpp [ 46%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerLowHash.cpp [ 47%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerConnectivityGraph.cpp [ 47%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LongBaseSequence.cpp [ 48%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o.d -o 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/build/shasta-McdAxI/shasta-0.8.0/src/LowHash1.cpp [ 49%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API -I/build/shasta-McdAxI/shasta-0.8.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/MarkerFinder.cpp 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/build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp: In member function ‘void shasta::Assembler::cleanupDuplicateMarkersPattern2(shasta::MarkerGraph::VertexId, uint64_t, uint64_t, bool, std::vector >&, std::vector&, bool, std::ostream&)’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp:463:40: warning: loop variable ‘markerDescriptor’ creates a copy from type ‘const MarkerDescriptor’ {aka ‘const std::pair’} [-Wrange-loop-construct] 463 | for(const MarkerDescriptor markerDescriptor: componentDescriptors) { | ^~~~~~~~~~~~~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp:463:40: note: use reference type to prevent copying 463 | for(const MarkerDescriptor markerDescriptor: componentDescriptors) { | ^~~~~~~~~~~~~~~~ | & [ 59%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o cd 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerOptions.cpp [ 69%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF 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/build/shasta-McdAxI/shasta-0.8.0/src/AssemblerOptions.cpp: In member function ‘void shasta::MarkerGraphOptions::parseSimplifyMaxLength()’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerOptions.cpp:1117:22: warning: loop variable ‘token’ creates a copy from type ‘const string’ {aka ‘const std::__cxx11::basic_string’} [-Wrange-loop-construct] 1117 | for(const string token: tokenizer) { | ^~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblerOptions.cpp:1117:22: note: use reference type to prevent copying 1117 | for(const string token: tokenizer) { | ^~~~~ | & [ 70%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. 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-I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyPathGraph2.cpp make[4]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' [ 72%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Bubbles.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Bubbles.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Bubbles.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Bubbles.cpp [ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o 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/build/shasta-McdAxI/shasta-0.8.0/src/CompressedAssemblyGraph.cpp [ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/ConfigurationTable.cpp [ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/ConsensusCaller.cpp [ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Coverage.cpp [ 76%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Forks.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Forks.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Forks.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Forks.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Forks.cpp [ 76%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Histogram.cpp /build/shasta-McdAxI/shasta-0.8.0/srcMain/main.cpp: In function ‘void shasta::main::listCommands()’: /build/shasta-McdAxI/shasta-0.8.0/srcMain/main.cpp:1591:22: warning: loop variable ‘command’ creates a copy from type ‘const string’ {aka ‘const std::__cxx11::basic_string’} [-Wrange-loop-construct] 1591 | for(const string command: commands) { | ^~~~~~~ /build/shasta-McdAxI/shasta-0.8.0/srcMain/main.cpp:1591:22: note: use reference type to prevent copying 1591 | for(const string command: commands) { | ^~~~~~~ | & [ 77%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ 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CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalAssemblyGraph.cpp [ 79%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalMarkerGraph-Write.cpp [ 80%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalMarkerGraph.cpp In file included from /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:2: In copy constructor ‘shasta::AssemblyGraph2Edge::Branch::Branch(const shasta::AssemblyGraph2Edge::Branch&)’, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Args = {const shasta::AssemblyGraph2Edge::Branch&}]’ at /usr/include/c++/11/bits/stl_construct.h:119:7, inlined from ‘static _ForwardIterator std::__uninitialized_fill_n<_TrivialValueType>::__uninit_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = shasta::AssemblyGraph2Edge::Branch*; _Size = long unsigned int; _Tp = shasta::AssemblyGraph2Edge::Branch; bool _TrivialValueType = false]’ at /usr/include/c++/11/bits/stl_uninitialized.h:237:18, inlined from ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = shasta::AssemblyGraph2Edge::Branch*; _Size = long unsigned int; _Tp = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/bits/stl_uninitialized.h:297:17, inlined from ‘_ForwardIterator std::__uninitialized_fill_n_a(_ForwardIterator, _Size, const _Tp&, std::allocator<_Tp2>&) [with _ForwardIterator = shasta::AssemblyGraph2Edge::Branch*; _Size = long unsigned int; _Tp = shasta::AssemblyGraph2Edge::Branch; _Tp2 = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/bits/stl_uninitialized.h:410:39, inlined from ‘void std::vector<_Tp, _Alloc>::_M_fill_initialize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/stl_vector.h:1596:33, inlined from ‘std::vector<_Tp, _Alloc>::vector(std::vector<_Tp, _Alloc>::size_type, const value_type&, const allocator_type&) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/stl_vector.h:525:27, inlined from ‘shasta::AssemblyGraph2Edge::AssemblyGraph2Edge(uint64_t, const MarkerGraphPath&, bool)’ at /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:142:17, inlined from ‘boost::adjacency_list::edge_descriptor shasta::AssemblyGraph2::addEdge(const MarkerGraphPath&, bool)’ at /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:497:9: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:90:11: warning: ‘*(const __vector(2) long unsigned int*)((char*)& + offsetof(shasta::AssemblyGraph2Edge::Branch, shasta::AssemblyGraph2Edge::Branch::minimumCoverage))’ may be used uninitialized [-Wmaybe-uninitialized] 90 | class Branch { | ^~~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp: In member function ‘boost::adjacency_list::edge_descriptor shasta::AssemblyGraph2::addEdge(const MarkerGraphPath&, bool)’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:142:64: note: ‘’ declared here 142 | id(id), branches(1, Branch(path, containsSecondaryEdges)) {} | ^ In constructor ‘shasta::AssemblyGraph2Edge::Branch::Branch(shasta::AssemblyGraph2Edge::Branch&&)’, inlined from ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = shasta::AssemblyGraph2Edge::Branch; _Args = {shasta::AssemblyGraph2Edge::Branch}; _Tp = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/ext/new_allocator.h:162:4, inlined from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = shasta::AssemblyGraph2Edge::Branch; _Args = {shasta::AssemblyGraph2Edge::Branch}; _Tp = shasta::AssemblyGraph2Edge::Branch]’ at /usr/include/c++/11/bits/alloc_traits.h:516:17, inlined from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {shasta::AssemblyGraph2Edge::Branch}; _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/vector.tcc:115:30, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = shasta::AssemblyGraph2Edge::Branch; _Alloc = std::allocator]’ at /usr/include/c++/11/bits/stl_vector.h:1204:21, inlined from ‘void shasta::AssemblyGraph2::handleSuperbubble0(shasta::AssemblyGraph2::Superbubble&)’ at /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:3565:35: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.hpp:90:11: warning: ‘*(__vector(2) long unsigned int*)((char*)& + offsetof(shasta::AssemblyGraph2Edge::Branch, shasta::AssemblyGraph2Edge::Branch::minimumCoverage))’ may be used uninitialized [-Wmaybe-uninitialized] 90 | class Branch { | ^~~~~~ /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp: In member function ‘void shasta::AssemblyGraph2::handleSuperbubble0(shasta::AssemblyGraph2::Superbubble&)’: /build/shasta-McdAxI/shasta-0.8.0/src/AssemblyGraph2.cpp:3565:85: note: ‘’ declared here 3565 | newEdge.branches.push_back(E::Branch(markerGraphPath, containsSecondaryEdges)); | ^ [ 80%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LocalReadGraph.cpp [ 81%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LongBaseSequence.cpp [ 81%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LowHash0.cpp [ 82%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/LowHash1.cpp [ 82%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/MarkerFinder.cpp [ 83%] Linking CXX executable shastaDynamic cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lspoa -lcpu_features -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.9 -lcrypt -lpthread -ldl -lutil -lm -lm make[4]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' [ 83%] Built target shastaDynamicExecutable [ 84%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/MarkerGraph.cpp [ 84%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o -MF 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/build/shasta-McdAxI/shasta-0.8.0/src/MemoryMappedVector.cpp [ 86%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/MultithreadedObject.cpp [ 86%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/MurmurHash2.cpp [ 87%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PalindromeQuality.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PalindromeQuality.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PalindromeQuality.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PalindromeQuality.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/PalindromeQuality.cpp [ 87%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/PeakFinder.cpp [ 88%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/PythonModule.cpp [ 89%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o.d -o 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0 -DNDEBUG -DSHASTA_HTTP_SERVER -I/build/shasta-McdAxI/shasta-0.8.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/shasta-McdAxI/shasta-0.8.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -c /build/shasta-McdAxI/shasta-0.8.0/src/Reads.cpp [ 90%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ 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[100%] Built target shastaStaticLibrary make[3]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v4.3.2 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 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... 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/build/shasta-McdAxI/shasta-0.8.0/debian/tmp/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/./shasta-install/bin/shasta.a -- Installing: /build/shasta-McdAxI/shasta-0.8.0/debian/tmp/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/./shasta-install/bin/shasta.so -- Installing: /build/shasta-McdAxI/shasta-0.8.0/debian/tmp/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu/./shasta-install/bin/shastaDynamic make[1]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0/obj-x86_64-linux-gnu' dh_install -i dh_installdocs -i dh_sphinxdoc -i dh_installchangelogs -i dh_installexamples -i dh_installman -i dh_python3 -i dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i debian/rules override_dh_missing make[1]: Entering directory '/build/shasta-McdAxI/shasta-0.8.0' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//build/shasta-McdAxI/shasta-0.8.0 dh_missing --list-missing make[1]: Leaving directory '/build/shasta-McdAxI/shasta-0.8.0' dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.8.0-2_all.deb'. dpkg-genbuildinfo --build=all -O../shasta_0.8.0-2_all.buildinfo dpkg-genchanges --build=all -O../shasta_0.8.0-2_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/shasta-McdAxI /tmp/shasta-0.8.0-2m1k3xm5w I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.pZztlBqNcQ... I: success in 1065.8349 seconds md5: python3-shasta-doc_0.8.0-2_all.deb: OK sha1: python3-shasta-doc_0.8.0-2_all.deb: OK sha256: python3-shasta-doc_0.8.0-2_all.deb: OK Checksums: OK