Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/i/ivar/ivar_1.3+dfsg-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/ivar-1.3+dfsg-1ehidy8zn/ivar_1.3+dfsg-1_all.buildinfo Get source package info: ivar=1.3+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/ivar/1.3+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-4 binutils-common=2.35.1-4 binutils-x86-64-linux-gnu=2.35.1-4 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-1 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.1-1 gcc=4:10.2.0-1 gcc-10=10.2.1-1 gcc-10-base=10.2.1-1 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.1-1 libatomic1=10.2.1-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1+b1 libbinutils=2.35.1-4 libblkid1=2.36.1-2 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-1 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-4 libctf0=2.35.1-4 libcurl3-gnutls=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-1 libgcc-s1=10.2.1-1 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-3 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libhts-dev=1.11-2 libhts3=1.11-2 libicu67=67.1-5 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.1-1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.1-1 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.1 libquadmath0=10.2.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3+b1 libselinux1=3.1-2+b2 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libssh2-1=1.9.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-1 libstdc++6=10.2.1-1 libsub-override-perl=0.09-2 libsystemd0=247.1-4 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.1-1 libubsan1=10.2.1-1 libuchardet0=0.0.7-1 libudev1=247.1-4 libunistring2=0.9.10-4 libuuid1=2.36.1-2 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 util-linux=2.36.1-2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201214T025122Z/ 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 ivar=1.3+dfsg-1 && mkdir -p /build/ivar-7ECTZl && dpkg-source --no-check -x /*.dsc /build/ivar-7ECTZl/ivar-1.3+dfsg && chown -R builduser:builduser /build/ivar-7ECTZl" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/ivar-7ECTZl/ivar-1.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607894339" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/ivar-7ECTZl /tmp/ivar-1.3+dfsg-1ehidy8zn bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201214T025122Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.jhzreeVY1A 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.jhzreeVY1A Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201214T025122Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201214T025122Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (912 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 ... 4616 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-5) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201214T025122Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.jhzreeVY1A Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201214T025122Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 21s (1076 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.jhzreeVY1A I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d ivar=1.3+dfsg-1 && mkdir -p /build/ivar-7ECTZl && dpkg-source --no-check -x /*.dsc /build/ivar-7ECTZl/ivar-1.3+dfsg && chown -R builduser:builduser /build/ivar-7ECTZl"' exec /tmp/mmdebstrap.jhzreeVY1A Reading package lists... NOTICE: 'ivar' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ivar.git Please use: git clone https://salsa.debian.org/med-team/ivar.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 675 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main ivar 1.3+dfsg-1 (dsc) [2036 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main ivar 1.3+dfsg-1 (tar) [630 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main ivar 1.3+dfsg-1 (diff) [43.0 kB] Fetched 675 kB in 1s (1158 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'ivar_1.3+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting ivar in /build/ivar-7ECTZl/ivar-1.3+dfsg dpkg-source: info: unpacking ivar_1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.3+dfsg-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/ivar-7ECTZl/ivar-1.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607894339" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.jhzreeVY1A dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai make[1]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' dh_clean debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i configure.ac:12: installing './compile' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure -i ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for main in -lhts... no checking for main in -lpthread... no checking for main in -lz... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... no checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... no checking for memmove... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -i make -j4 make[1]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make all-recursive make[2]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' Making all in src make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp Using built-in specs. Using built-in specs. COLLECT_GCC=g++ COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Target: x86_64-linux-gnu Thread model: posix Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Supported LTO compression algorithms: zlib zstdThread model: posix Supported LTO compression algorithms: zlibgcc version 10.2.1 20201207 (Debian 10.2.1-1) zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cppCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' -quiet -dumpbase alignment.cpp -mtune=generic -march=x86-64 -auxbase-strip alignment.o -g -Wdate-time -Wall /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -Wextra -Werror -quiet -std=c++11 -v -version -I -fasynchronous-unwind-tables . -o -I /tmp/cchkyuQF.s .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -mtune=generic -march=x86-64 -auxbase-strip suffix_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccBlQieL.s Using built-in specs. Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 COLLECT_GCC=g++ Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstdOFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa gcc version 10.2.1 20201207 (Debian 10.2.1-1) OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -imultiarch -quiet x86_64-linux-gnu -v -I -D_GNU_SOURCE . -D -I .. HAVE_CONFIG_H -imultiarch x86_64-linux-gnu -D -D_GNU_SOURCE _FORTIFY_SOURCE=2 -D HAVE_CONFIG_H ivar.cpp -D -quiet _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -dumpbase -quiet ivar.cpp -dumpbase call_consensus_pileup.cpp -mtune=generic -mtune=generic -march=x86-64 -march=x86-64 -auxbase-strip -auxbase-strip call_consensus_pileup.o ivar.o -g -Wdate-time -g -Wall -Wdate-time -Wextra -Wall -Werror -Wextra -std=c++11 -Werror -version -std=c++11 -fasynchronous-unwind-tables -version -o /tmp/cc72X6Jy.s -fasynchronous-unwind-tables -o /tmp/ccLaoYXw.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, b9aa696cd60a4f GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o alignment.o /tmp/cchkyuQF.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -mtune=generic -march=x86-64 -auxbase-strip trim_primer_quality.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccOnUnJ9.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o suffix_tree.o /tmp/ccBlQieL.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -mtune=generic -march=x86-64 -auxbase-strip remove_reads_from_amplicon.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccGQlHQq.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o call_consensus_pileup.o /tmp/cc72X6Jy.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o ivar.o /tmp/ccLaoYXw.s Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -mtune=generic -march=x86-64 -auxbase-strip call_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc3zU82C.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -mtune=generic -march=x86-64 -auxbase-strip primer_bed.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccKrk9NP.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o trim_primer_quality.o /tmp/ccOnUnJ9.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -mtune=generic -march=x86-64 -auxbase-strip allele_functions.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccUQHzf7.s COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o remove_reads_from_amplicon.o /tmp/ccGQlHQq.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -mtune=generic -march=x86-64 -auxbase-strip get_masked_amplicons.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccqsDGMl.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o get_masked_amplicons.o /tmp/ccqsDGMl.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -mtune=generic -march=x86-64 -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccE1TaKv.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o primer_bed.o /tmp/ccKrk9NP.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o allele_functions.o /tmp/ccUQHzf7.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mtune=generic -march=x86-64 -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc1OEdiQ.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -mtune=generic -march=x86-64 -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccEXxMk0.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o call_variants.o /tmp/cc3zU82C.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -mtune=generic -march=x86-64 -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc7extZe.s GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/10/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/x86_64-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/x86_64-linux-gnu/10/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-1) version 10.2.1 20201207 (x86_64-linux-gnu) compiled by GNU C version 10.2.1 20201207, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: b0ce43b702b13c00b4b9aa696cd60a4f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o get_common_variants.o /tmp/ccE1TaKv.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o interval_tree.o /tmp/cc7extZe.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o ref_seq.o /tmp/ccEXxMk0.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as -v -I . -I .. --64 -o parse_gff.o /tmp/cc1OEdiQ.s GNU assembler version 2.35.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.1 MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' g++ -v -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) MAKEFLAGS=w -j4 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccDWVNyL.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' Making all in tests make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[2]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[1]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' dh_auto_test --no-parallel make -j1 check VERBOSE=1 make[2]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' Making check in src make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' Making check in tests make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search make[4]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread make[4]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make check-TESTS make[4]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[5]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' PASS: check_primer_trim PASS: check_trim PASS: check_quality_trim PASS: check_consensus PASS: check_allele_depth PASS: check_consensus_threshold PASS: check_consensus_min_depth PASS: check_consensus_seq_id PASS: check_primer_bed PASS: check_getmasked PASS: check_removereads PASS: check_variants PASS: check_common_variants PASS: check_unpaired_trim PASS: check_primer_trim_edge_cases PASS: check_isize_trim PASS: check_interval_tree PASS: check_amplicon_search ============================================================================ Testsuite summary for ivar 1.3 ============================================================================ # TOTAL: 18 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[4]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[2]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[1]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -i dh_auto_install -i make -j4 install DESTDIR=/build/ivar-7ECTZl/ivar-1.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' Making install in src make[2]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' g++ -v -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-hqdHUA/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20201207 (Debian 10.2.1-1) MAKEFLAGS=w -j4 -- DESTDIR=/build/ivar-7ECTZl/ivar-1.3+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/10/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccMIJEbX.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/ivar-7ECTZl/ivar-1.3+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ivar '/build/ivar-7ECTZl/ivar-1.3+dfsg/debian/tmp/usr/bin' make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' make[2]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/src' Making install in tests make[2]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[2]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg/tests' make[2]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[3]: Entering directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[2]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' make[1]: Leaving directory '/build/ivar-7ECTZl/ivar-1.3+dfsg' dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installexamples -i dh_installman -i dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.3+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../ivar_1.3+dfsg-1_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/ivar-7ECTZl /tmp/ivar-1.3+dfsg-1ehidy8zn I: cleaning package lists and apt cache... W: deleting files in /tmp: trim.bam I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.jhzreeVY1A... I: success in 526.6762 seconds md5: ivar-doc_1.3+dfsg-1_all.deb: OK sha1: ivar-doc_1.3+dfsg-1_all.deb: OK sha256: ivar-doc_1.3+dfsg-1_all.deb: OK Checksums: OK