DC-Build-Header: stacks 1.46-1 / 2017-08-20 18:48:07 +0000 DC-Task: type:rebuild-binarch-only source:stacks version:1.46-1 chroot:unstable esttime:116 logfile:/tmp/stacks_1.46-1_unstable_clang5.0.log modes:clang50:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang50 stacks_1.46-1' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-42-79.eu-central-1.compute.internal +==============================================================================+ | stacks 1.46-1 (amd64) Sun, 20 Aug 2017 18:48:07 +0000 | +==============================================================================+ Package: stacks Version: 1.46-1 Source Version: 1.46-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-e082dd6e-fd94-46bb-b716-ec528f279d26' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang50 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=5.0 + echo 'Install of clang-5.0' Install of clang-5.0 + apt-get update Hit:1 http://127.0.0.1:9999/debian unstable InRelease Get:2 http://127.0.0.1:9999/debian unstable/main Translation-en [5785 kB] Fetched 5785 kB in 1s (3999 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-5.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libasan3 libbsd0 libclang-common-5.0-dev libclang1-5.0 libedit2 libgcc-6-dev libjsoncpp1 libllvm5.0 libncurses5 libobjc-6-dev libobjc4 libstdc++-6-dev Suggested packages: gnustep gnustep-devel clang-5.0-doc libomp-dev libstdc++-6-doc Recommended packages: llvm-5.0-dev python libgpm2 The following NEW packages will be installed: clang-5.0 libasan3 libbsd0 libclang-common-5.0-dev libclang1-5.0 libedit2 libgcc-6-dev libjsoncpp1 libllvm5.0 libncurses5 libobjc-6-dev libobjc4 libstdc++-6-dev 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 88.4 MB of archives. After this operation, 376 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.6-1 [90.3 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20170715-2 [93.8 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm5.0 amd64 1:5.0~+rc2-1 [13.5 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-5.0 amd64 1:5.0~+rc2-1 [6729 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libasan3 amd64 6.4.0-3 [311 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libgcc-6-dev amd64 6.4.0-3 [2296 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libstdc++-6-dev amd64 6.4.0-3 [1421 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.2.0-1 [51.0 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-3 [197 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-5.0-dev amd64 1:5.0~+rc2-1 [1989 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 clang-5.0 amd64 1:5.0~+rc2-1 [61.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 88.4 MB in 0s (98.8 MB/s) Selecting previously unselected package libbsd0: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 ... 9822 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.6-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.6-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../01-libncurses5_6.0+20170715-2_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20170715-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../02-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm5.0:amd64. Preparing to unpack .../03-libllvm5.0_1%3a5.0~+rc2-1_amd64.deb ... Unpacking libllvm5.0:amd64 (1:5.0~+rc2-1) ... Selecting previously unselected package libclang1-5.0:amd64. Preparing to unpack .../04-libclang1-5.0_1%3a5.0~+rc2-1_amd64.deb ... Unpacking libclang1-5.0:amd64 (1:5.0~+rc2-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../05-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libasan3:amd64. Preparing to unpack .../06-libasan3_6.4.0-3_amd64.deb ... Unpacking libasan3:amd64 (6.4.0-3) ... Selecting previously unselected package libgcc-6-dev:amd64. Preparing to unpack .../07-libgcc-6-dev_6.4.0-3_amd64.deb ... Unpacking libgcc-6-dev:amd64 (6.4.0-3) ... Selecting previously unselected package libstdc++-6-dev:amd64. Preparing to unpack .../08-libstdc++-6-dev_6.4.0-3_amd64.deb ... Unpacking libstdc++-6-dev:amd64 (6.4.0-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../09-libobjc4_7.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (7.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../10-libobjc-6-dev_6.4.0-3_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.4.0-3) ... Selecting previously unselected package libclang-common-5.0-dev. Preparing to unpack .../11-libclang-common-5.0-dev_1%3a5.0~+rc2-1_amd64.deb ... Unpacking libclang-common-5.0-dev (1:5.0~+rc2-1) ... Selecting previously unselected package clang-5.0. Preparing to unpack .../12-clang-5.0_1%3a5.0~+rc2-1_amd64.deb ... Unpacking clang-5.0 (1:5.0~+rc2-1) ... Setting up libncurses5:amd64 (6.0+20170715-2) ... Setting up libobjc4:amd64 (7.2.0-1) ... Setting up libasan3:amd64 (6.4.0-3) ... Setting up libgcc-6-dev:amd64 (6.4.0-3) ... Setting up libstdc++-6-dev:amd64 (6.4.0-3) ... Setting up libbsd0:amd64 (0.8.6-1) ... Processing triggers for libc-bin (2.24-14) ... Setting up libobjc-6-dev:amd64 (6.4.0-3) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm5.0:amd64 (1:5.0~+rc2-1) ... Setting up libclang1-5.0:amd64 (1:5.0~+rc2-1) ... Setting up libclang-common-5.0-dev (1:5.0~+rc2-1) ... Setting up clang-5.0 (1:5.0~+rc2-1) ... Processing triggers for libc-bin (2.24-14) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-5.0 g++-4.6 + ln -s clang-5.0 gcc-4.6 + ln -s clang-5.0 cpp-4.6 + ln -s clang-5.0 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-5.0 g++-4.7 + ln -s clang-5.0 gcc-4.7 + ln -s clang-5.0 cpp-4.7 + ln -s clang-5.0 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-5.0 g++-4.8 + ln -s clang-5.0 gcc-4.8 + ln -s clang-5.0 cpp-4.8 + ln -s clang-5.0 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-5.0 g++-4.9 + ln -s clang-5.0 gcc-4.9 + ln -s clang-5.0 cpp-4.9 + ln -s clang-5.0 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-5.0 g++-5 + ln -s clang-5.0 gcc-5 + ln -s clang-5.0 cpp-5 + ln -s clang-5.0 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-5.0 g++-6 + ln -s clang-5.0 gcc-6 + ln -s clang-5.0 cpp-6 + ln -s clang-5.0 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-5.0 g++-7 + ln -s clang-5.0 gcc-7 + ln -s clang-5.0 cpp-7 + ln -s clang-5.0 gcc + echo 'gcc-7 hold' + dpkg --set-selections + echo 'g++-7 hold' + dpkg --set-selections + cd - /build/stacks-Z6PpuR + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang50'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'stacks' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/stacks.git Please use: git clone https://anonscm.debian.org/git/debian-med/stacks.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 918 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main stacks 1.46-1 (dsc) [2082 B] Get:2 http://127.0.0.1:9999/debian unstable/main stacks 1.46-1 (tar) [907 kB] Get:3 http://127.0.0.1:9999/debian unstable/main stacks 1.46-1 (diff) [8780 B] Fetched 918 kB in 0s (4131 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/stacks-Z6PpuR/stacks-1.46' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-Z6PpuR' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Kg2Htr/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-Kg2Htr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Kg2Htr/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Kg2Htr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Kg2Htr/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-Kg2Htr/apt_archive ./ Packages [434 B] Fetched 1740 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 784 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Kg2Htr/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 784 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11331 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 10), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools Filtered Build-Depends: debhelper (>= 10), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<>/resolver-Kg2Htr/apt_archive/sbuild-build-depends-stacks-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-stacks-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-Kg2Htr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Kg2Htr/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Kg2Htr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Kg2Htr/apt_archive ./ Sources [525 B] Get:5 copy:/<>/resolver-Kg2Htr/apt_archive ./ Packages [605 B] Fetched 2093 B in 0s (0 B/s) Reading package lists... Reading package lists... Install stacks build dependencies (apt-based resolver) ------------------------------------------------------ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.1 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx-cur ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.1 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common samtools sbuild-build-depends-stacks-dummy zlib1g-dev 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 28.6 MB of archives. After this operation, 95.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Kg2Htr/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [824 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.2-1 [28.3 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.13-4 [392 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 python2.7-minimal amd64 2.7.13-4 [1370 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 mime-support all 3.60 [36.7 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.3-1 [87.5 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.19.3-3 [582 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.1 amd64 1.1.0f-4 [1349 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.13-4 [1898 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 python2.7 amd64 2.7.13-4 [292 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.31-1 [223 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.31-1 [112 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.31-1 [64.2 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15.1-2 [62.2 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15.1-2 [120 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15.1-2 [312 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15.1-2 [155 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.45+dfsg-1 [87.0 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.45+dfsg-1 [223 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.038-1 [11.1 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.53.4-3 [2796 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.7.2 [975 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libbam-dev amd64 0.1.19-2 [123 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.24.0-1 [81.6 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.18.0-2 [43.4 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.55.0-1 [294 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libhts2 amd64 1.5-1 [293 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 samtools amd64 1.5-1 [263 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.6 MB in 0s (54.6 MB/s) Selecting previously unselected package groff-base. (Reading database ... 11331 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.2-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.2-1) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../04-libpython2.7-minimal_2.7.13-4_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-4) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../05-python2.7-minimal_2.7.13-4_amd64.deb ... Unpacking python2.7-minimal (2.7.13-4) ... 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Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up libpipeline1:amd64 (1.4.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libmagic-mgc (1:5.31-1) ... Setting up libmagic1:amd64 (1:5.31-1) ... Setting up libcroco3:amd64 (0.6.12-1) ... Setting up libssh2-1:amd64 (1.8.0-1) ... Processing triggers for libc-bin (2.24-14) ... Setting up autotools-dev (20161112.1) ... Setting up libldap-2.4-2:amd64 (2.4.45+dfsg-1) ... Setting up libssl1.1:amd64 (1.1.0f-4) ... Setting up libbam-dev (0.1.19-2) ... Setting up libsqlite3-0:amd64 (3.19.3-3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.12+nmu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpython2.7-stdlib:amd64 (2.7.13-4) ... Setting up autopoint (0.19.8.1-2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up python2.7 (2.7.13-4) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.31-1) ... Setting up libkrb5support0:amd64 (1.15.1-2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up libk5crypto3:amd64 (1.15.1-2) ... Setting up po-debconf (1.0.20) ... Setting up libkrb5-3:amd64 (1.15.1-2) ... Setting up libgssapi-krb5-2:amd64 (1.15.1-2) ... Setting up libcurl3-gnutls:amd64 (7.55.0-1) ... Setting up libhts2:amd64 (1.5-1) ... Setting up samtools (1.5-1) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.7.2) ... Setting up dh-autoreconf (14) ... Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-14) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.29-4 dpkg-dev_1.18.24 g++-7_7.2.0-1 gcc-7_7.2.0-1 libc6-dev_2.24-14 libstdc++-6-dev_6.4.0-3 libstdc++-7-dev_7.2.0-1 libstdc++6_7.2.0-1 linux-libc-dev_4.12.6-1 Package versions: adduser_3.116 apt_1.5~beta2 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.29-4 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-4 build-essential_12.3 bzip2_1.0.6-8.1 clang-5.0_1:5.0~+rc2-1 coreutils_8.26-3 cpp_4:7.1.0-2 cpp-7_7.2.0-1 dash_0.5.8-2.5 debconf_1.5.63 debfoster_2.7-2.1+b1 debhelper_10.7.2 debian-archive-keyring_2017.5 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 eatmydata_105-5 fakeroot_1.22-1 fdisk_2.29.2-4 file_1:5.31-1 findutils_4.6.0+git+20170729-2 g++_4:7.1.0-2 g++-7_7.2.0-1 gcc_4:7.1.0-2 gcc-6-base_6.4.0-3 gcc-7_7.2.0-1 gcc-7-base_7.2.0-1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.23-2 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hostname_3.18+b1 init-system-helpers_1.49 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta2 libarchive-zip-perl_1.59-1 libasan3_6.4.0-3 libasan4_7.2.0-1 libatomic1_7.2.0-1 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b2 libbam-dev_0.1.19-2 libblkid1_2.29.2-4 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3+b1 libcc1-0_7.2.0-1 libcilkrts5_7.2.0-1 libclang-common-5.0-dev_1:5.0~+rc2-1 libclang1-5.0_1:5.0~+rc2-1 libcomerr2_1.43.5-1 libcroco3_0.6.12-1 libcurl3-gnutls_7.55.0-1 libdb5.3_5.3.28-13 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.3-1 libfakeroot_1.22-1 libfdisk1_2.29.2-4 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-3 libgcc-7-dev_7.2.0-1 libgcc1_1:7.2.0-1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-3 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-3 libgomp1_7.2.0-1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-1+b1 libhts2_1.5-1 libicu57_57.1-6 libidn2-0_2.0.2-3 libisl15_0.18-1 libitm1_7.2.0-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libllvm5.0_1:5.0~+rc2-1 liblsan0_7.2.0-1 liblz4-1_0.0~r131-2+b1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.31-1 libmagic1_1:5.31-1 libmount1_2.29.2-4 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.2.0-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1+b1 libnghttp2-14_1.24.0-1 libobjc-6-dev_6.4.0-3 libobjc4_7.2.0-1 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.26_5.26.0-5 libpipeline1_1.4.2-1 libpsl5_0.18.0-2 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-4 libpython2.7-stdlib_2.7.13-4 libquadmath0_7.2.0-1 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-4 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.19.3-3 libss2_1.43.5-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-4 libstdc++-6-dev_6.4.0-3 libstdc++-7-dev_7.2.0-1 libstdc++6_7.2.0-1 libsystemd0_234-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libtsan0_7.2.0-1 libubsan0_7.2.0-1 libudev1_234-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-4 libxml2_2.9.4+dfsg1-3 linux-libc-dev_4.12.6-1 login_1:4.4-4.1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mime-support_3.60 mount_2.29.2-4 multiarch-support_2.24-14 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.26.0-5 perl-base_5.26.0-5 perl-modules-5.26_5.26.0-5 po-debconf_1.0.20 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-4 python2.7-minimal_2.7.13-4 readline-common_7.0-3 samtools_1.5-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 util-linux_2.29.2-4 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jun 24 07:01:46 2017 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./stacks_1.46-1.dsc dpkg-source: info: extracting stacks in /<> dpkg-source: info: unpacking stacks_1.46.orig.tar.gz dpkg-source: info: unpacking stacks_1.46-1.debian.tar.xz dpkg-source: info: applying constants.php.patch dpkg-source: info: applying email-settings.patch dpkg-source: info: applying script-exe-paths Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-e082dd6e-fd94-46bb-b716-ec528f279d26 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 1.46-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build stacks-1.46 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 dh_auto_clean dh_autoreconf_clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f ./constants.php make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --with python2 dh_update_autotools_config -a dh_autoreconf -a parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib configure: WARNING: unrecognized options: --disable-maintainer-mode, --with-bam-include-path, --with-bam-lib-path 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 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 for style of include used by make... GNU 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 whether g++ supports C++11 features by default... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes 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 float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for gcc option to support OpenMP... unsupported checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for functional regular expressions... yes checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode, --with-bam-include-path, --with-bam-lib-path make[1]: Leaving directory '/<>' dh_auto_build -a make -j16 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in htslib make[3]: Entering directory '/<>/htslib' echo '/* Empty config.h generated by Makefile */' > config.h echo '#define HTS_VERSION "1.3.1"' > version.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c gcc -g -Wall -O2 -I. -c -o hts.o hts.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c hts.c:48:5: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT2(, BGZF*, bgzf_read, 65536) ^ ./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2' __KS_INLINED(__read) ^ ./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED' static inline int ks_getc(kstream_t *ks) \ ^ gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~^~~~~~~~~~~~~~~~~ cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:388: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~^~~~~ cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~^~~~~~~~~~~~~~~~~ cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:388: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~^~~~~ gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c gcc -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c gcc -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.c 1 warning generated. 8 warnings generated. ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a make[3]: Leaving directory '/<>/htslib' Making all in . make[3]: Entering directory '/<>' g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-cmb.o `test -f 'src/cmb.cc' || echo './'`src/cmb.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-pstacks.o `test -f 'src/pstacks.cc' || echo './'`src/pstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-estacks.o `test -f 'src/estacks.cc' || echo './'`src/estacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-cstacks.o `test -f 'src/cstacks.cc' || echo './'`src/cstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-sstacks.o `test -f 'src/sstacks.cc' || echo './'`src/sstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-rxstacks.o `test -f 'src/rxstacks.cc' || echo './'`src/rxstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-hstacks.o `test -f 'src/hstacks.cc' || echo './'`src/hstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-process_radtags.o `test -f 'src/process_radtags.cc' || echo './'`src/process_radtags.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-write.o `test -f 'src/write.cc' || echo './'`src/write.cc src/process_radtags.cc:767:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] realpath(in_path_1.c_str(), abspath); ^~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-process_shortreads.o `test -f 'src/process_shortreads.cc' || echo './'`src/process_shortreads.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-write.o `test -f 'src/write.cc' || echo './'`src/write.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-kmer_filter.o `test -f 'src/kmer_filter.cc' || echo './'`src/kmer_filter.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-write.o `test -f 'src/write.cc' || echo './'`src/write.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-clone_filter.o `test -f 'src/clone_filter.cc' || echo './'`src/clone_filter.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-write.o `test -f 'src/write.cc' || echo './'`src/write.cc 1 warning generated. g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-genotypes.o `test -f 'src/genotypes.cc' || echo './'`src/genotypes.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-populations.o `test -f 'src/populations.cc' || echo './'`src/populations.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-export_formats.o `test -f 'src/export_formats.cc' || echo './'`src/export_formats.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-Vcf.o `test -f 'src/Vcf.cc' || echo './'`src/Vcf.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-phasedstacks.o `test -f 'src/phasedstacks.cc' || echo './'`src/phasedstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks-ustacks.o src/ustacks-stacks.o src/ustacks-constants.o src/ustacks-mstack.o src/ustacks-mst.o src/ustacks-cmb.o src/ustacks-DNASeq.o src/ustacks-DNANSeq.o src/ustacks-models.o src/ustacks-utils.o src/ustacks-kmers.o src/ustacks-aln_utils.o src/ustacks-input.o -lz -lgomp g++ -std=gnu++11 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pstacks src/pstacks-pstacks.o src/pstacks-stacks.o src/pstacks-constants.o src/pstacks-mstack.o src/pstacks-log_utils.o src/pstacks-DNANSeq.o src/pstacks-DNASeq.o src/pstacks-models.o src/pstacks-utils.o src/pstacks-aln_utils.o src/pstacks-input.o ./htslib/libhts.a -lz -lgomp /usr/bin/ld: ./htslib/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_kill@@GLIBC_2.2.5' //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:1283: recipe for target 'pstacks' failed make[3]: *** [pstacks] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/<>' Makefile:3793: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/<>' Makefile:911: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: make -j16 returned exit code 2 debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-08-20T18:49:37Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 188628 Build-Time: 60 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 8 Job: stacks_1.46-1 Machine Architecture: amd64 Package: stacks Package-Time: 90 Source-Version: 1.46-1 Space: 188628 Status: attempted Version: 1.46-1 -------------------------------------------------------------------------------- Finished at 2017-08-20T18:49:37Z Build needed 00:01:30, 188628k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 90.821064022s