DC-Build-Header: sga 0.10.14-3 / 2016-08-29 16:58:59 +0000 DC-Task: type:rebuild-binarch-only source:sga version:0.10.14-3 chroot:unstable esttime:180 logfile:/tmp/sga_0.10.14-3_unstable_clang3.8.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang sga_0.10.14-3' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-6-92.eu-central-1.compute.internal +==============================================================================+ | sga 0.10.14-3 (amd64) Mon, 29 Aug 2016 16:58:59 +0000 | +==============================================================================+ Package: sga Version: 0.10.14-3 Source Version: 0.10.14-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-ca2d9914-846f-4973-a3a1-714ed5b4dc33' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.8 + echo 'Install of clang-3.8' Install of clang-3.8 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [209 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en [5451 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0319.00.pdiff [16.7 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0319.00.pdiff [13.2 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Fetched 5755 kB in 3s (1576 kB/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges + apt-get install --yes --no-install-recommends --force-yes clang-3.8 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.8-doc Recommended packages: llvm-3.8-dev python The following NEW packages will be installed: clang-3.8 libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. Need to get 38.3 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20150325-1+b1 [85.2 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.8 amd64 1:3.8.1-9 [10.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 6.2.0-1 [110 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.2.0-1 [394 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.8 amd64 1:3.8.1-9 [4188 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.8-dev amd64 1:3.8.1-9 [1477 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.8 amd64 1:3.8.1-9 [21.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.3 MB in 2s (18.5 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 ... 9446 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../1-libedit2_3.1-20150325-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20150325-1+b1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../2-libffi6_3.2.1-4_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-4) ... Selecting previously unselected package libllvm3.8:amd64. Preparing to unpack .../3-libllvm3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libllvm3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../4-libobjc4_6.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (6.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../5-libobjc-6-dev_6.2.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.2.0-1) ... Selecting previously unselected package libclang1-3.8:amd64. Preparing to unpack .../6-libclang1-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libclang1-3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libclang-common-3.8-dev. Preparing to unpack .../7-libclang-common-3.8-dev_1%3a3.8.1-9_amd64.deb ... Unpacking libclang-common-3.8-dev (1:3.8.1-9) ... Selecting previously unselected package clang-3.8. Preparing to unpack .../8-clang-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking clang-3.8 (1:3.8.1-9) ... Setting up libobjc4:amd64 (6.2.0-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up libobjc-6-dev:amd64 (6.2.0-1) ... Setting up libffi6:amd64 (3.2.1-4) ... Setting up libedit2:amd64 (3.1-20150325-1+b1) ... Setting up libllvm3.8:amd64 (1:3.8.1-9) ... Setting up libclang-common-3.8-dev (1:3.8.1-9) ... Setting up libclang1-3.8:amd64 (1:3.8.1-9) ... Setting up clang-3.8 (1:3.8.1-9) ... Processing triggers for libc-bin (2.23-5) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. W: No sandbox user '_apt' on the system, can not drop privileges + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.8 g++-4.6 + ln -s clang-3.8 gcc-4.6 + ln -s clang-3.8 cpp-4.6 + ln -s clang-3.8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.8 g++-4.7 + ln -s clang-3.8 gcc-4.7 + ln -s clang-3.8 cpp-4.7 + ln -s clang-3.8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.8 g++-4.8 + ln -s clang-3.8 gcc-4.8 + ln -s clang-3.8 cpp-4.8 + ln -s clang-3.8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.8 g++-4.9 + ln -s clang-3.8 gcc-4.9 + ln -s clang-3.8 cpp-4.9 + ln -s clang-3.8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.8 g++-5 + ln -s clang-3.8 gcc-5 + ln -s clang-3.8 cpp-5 + ln -s clang-3.8 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.8 g++-6 + ln -s clang-3.8 gcc-6 + ln -s clang-3.8 cpp-6 + ln -s clang-3.8 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + cd - /build/sga-DTV4i0 + 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/clang'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: linux-libc-dev 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1158 kB of archives. After this operation, 60.4 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 linux-libc-dev amd64 4.7.2-1 [1158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1158 kB in 0s (70.3 MB/s) (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 ... 9769 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_4.7.2-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.7.2-1) over (4.6.4-1) ... Setting up linux-libc-dev:amd64 (4.7.2-1) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'sga' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/sga.git Please use: git clone https://anonscm.debian.org/git/debian-med/sga.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6780 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main sga 0.10.14-3 (dsc) [2058 B] Get:2 http://127.0.0.1:9999/debian unstable/main sga 0.10.14-3 (tar) [6567 kB] Get:3 http://127.0.0.1:9999/debian unstable/main sga 0.10.14-3 (diff) [211 kB] Fetched 6780 kB in 0s (24.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/sga-DTV4i0/sga-0.10.14' with '<>' I: NOTICE: Log filtering will replace 'build/sga-DTV4i0' 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-Dd1BJq/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-Dd1BJq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Dd1BJq/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Dd1BJq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Dd1BJq/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-Dd1BJq/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges 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 776 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Dd1BJq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 776 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 9775 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) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9.0.0), dh-autoreconf, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, gawk, help2man, samtools, python, python-ruffus, python-pysam Filtered Build-Depends: debhelper (>= 9.0.0), dh-autoreconf, libsparsehash-dev, zlib1g-dev, libbamtools-dev, gawk, help2man, samtools, python, python-ruffus, python-pysam dpkg-deb: building package 'sbuild-build-depends-sga-dummy' in '/<>/resolver-4MN4cZ/apt_archive/sbuild-build-depends-sga-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-sga-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-4MN4cZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4MN4cZ/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-4MN4cZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4MN4cZ/apt_archive ./ Sources [420 B] Get:5 copy:/<>/resolver-4MN4cZ/apt_archive ./ Packages [502 B] Fetched 1879 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Install sga 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 fontconfig fontconfig-config fonts-dejavu-core gawk gettext gettext-base graphviz groff-base help2man intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.4.0 libcairo2 libcdt5 libcgraph6 libcroco3 libcurl3-gnutls libdatrie1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libglib2.0-0 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhogweed4 libhts1 libice6 libicu57 libidn11 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libthai-data libthai0 libtiff5 libtimedate-perl libtool libunistring0 libwebp6 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 lsb-base m4 man-db mime-support po-debconf python python-minimal python-pysam python-ruffus python2.7 python2.7-minimal readline-common samtools ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gawk-doc gettext-doc libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff libbamtools-doc libgd-tools gnutls-bin krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl python-doc python-tk python-drmaa python2.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx-cur fonts-liberation ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs libgts-bin krb5-locales libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gawk gettext gettext-base graphviz groff-base help2man intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.4.0 libcairo2 libcdt5 libcgraph6 libcroco3 libcurl3-gnutls libdatrie1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libglib2.0-0 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhogweed4 libhts1 libice6 libicu57 libidn11 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libthai-data libthai0 libtiff5 libtimedate-perl libtool libunistring0 libwebp6 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 lsb-base m4 man-db mime-support po-debconf python python-minimal python-pysam python-ruffus python2.7 python2.7-minimal readline-common samtools sbuild-build-depends-sga-dummy ucf x11-common zlib1g-dev 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 43.1 MB of archives. After this operation, 141 MB of additional disk space will be used. Get:1 copy:/<>/resolver-4MN4cZ/apt_archive ./ sbuild-build-depends-sga-dummy 0.invalid.0 [846 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-8 [1162 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.5-1 [1003 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.12-2 [387 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 python2.7-minimal amd64 2.7.12-2 [1348 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 python-minimal amd64 2.7.11-2 [40.3 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 2.2.0-1 [82.0 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 6.3-8 [57.7 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libreadline6 amd64 6.3-8+b4 [142 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.14.1-1 [559 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2h-1 [1287 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.12-2 [1875 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 python2.7 amd64 2.7.12-2 [277 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libpython-stdlib amd64 2.7.11-2 [19.8 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 python amd64 2.7.11-2 [153 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libpng16-16 amd64 1.6.24-2 [279 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libfreetype6 amd64 2.6.3-3+b1 [437 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 ucf all 3.0036 [70.2 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libfontconfig1 amd64 2.11.0-6.7 [331 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig amd64 2.11.0-6.7 [403 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 gawk amd64 1:4.1.3+dfsg-0.1 [545 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-1.2 [158 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20160629 [27.6 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 x11-common all 1:7.7+16 [251 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libice6 amd64 2:1.0.9-1+b1 [58.8 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3 [18.4 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libsm6 amd64 2:1.2.2-1+b1 [33.6 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [26.2 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1 amd64 1.11.1-1.1 [45.3 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libx11-data all 2:1.6.3-1 [128 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libx11-6 amd64 2:1.6.3-1 [742 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1 [52.7 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libxpm4 amd64 1:3.5.11-1+b1 [48.1 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libjbig0 amd64 2.1-3.1 [30.7 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-5 [111 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.9-4 [50.0 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.3-3 [801 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.14.3+dfsg-1 [61.0 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.14.3+dfsg-1 [115 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.14.3+dfsg-1 [311 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.14.3+dfsg-1 [154 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 libcdt5 amd64 2.38.0-15 [59.4 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 libcgraph6 amd64 2.38.0-15 [82.0 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.0-1 [132 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libtiff5 amd64 4.0.6-2 [222 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 libwebp6 amd64 0.5.1-2 [235 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 libgd3 amd64 2.2.3-3+b1 [136 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 libpixman-1-0 amd64 0.33.6-1 [532 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-render0 amd64 1.11.1-1.1 [17.5 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shm0 amd64 1.11.1-1.1 [11.6 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libxrender1 amd64 1:0.9.9-2 [31.8 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libcairo2 amd64 1.14.6-1+b1 [767 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libthai-data all 0.1.25-1 [165 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libdatrie1 amd64 0.2.10-2 [35.8 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libthai0 amd64 0.1.25-1 [51.6 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libpango-1.0-0 amd64 1.40.1-1 [311 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libgraphite2-3 amd64 1.3.8-1 [76.4 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libharfbuzz0b amd64 1.2.7-1+b1 [612 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.40.1-1 [236 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.40.1-1 [223 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libpathplan4 amd64 2.38.0-15 [62.6 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libxdot4 amd64 2.38.0-15 [55.4 kB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 libgvc6 amd64 2.38.0-15 [637 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 libgvpr2 amd64 2.38.0-15 [210 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1 [200 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 graphviz amd64 2.38.0-15 [733 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 help2man amd64 1.47.4 [162 kB] Get:109 http://127.0.0.1:9999/debian unstable/main amd64 libbamtools2.4.0 amd64 2.4.0+dfsg-6 [190 kB] Get:110 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Get:111 http://127.0.0.1:9999/debian unstable/main amd64 libbamtools-dev amd64 2.4.0+dfsg-6 [230 kB] Get:112 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.13.0-1 [79.4 kB] Get:113 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [60.0 kB] Get:114 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB] Get:115 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.50.1-1 [278 kB] Get:116 http://127.0.0.1:9999/debian unstable/main amd64 libhts1 amd64 1.3.1-2 [256 kB] Get:117 http://127.0.0.1:9999/debian unstable/main amd64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get:118 http://127.0.0.1:9999/debian unstable/main amd64 python-pysam amd64 0.9.1.4+ds-1 [1114 kB] Get:119 http://127.0.0.1:9999/debian unstable/main amd64 python-ruffus all 2.6.3+dfsg-4 [98.3 kB] Get:120 http://127.0.0.1:9999/debian unstable/main amd64 samtools amd64 1.3.1-2 [251 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.1 MB in 0s (53.6 MB/s) Selecting previously unselected package groff-base. (Reading database ... 9775 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-8_amd64.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.10_amd64.deb ... Unpacking bsdmainutils (9.0.10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.5-1_amd64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../04-libpython2.7-minimal_2.7.12-2_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.12-2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../05-python2.7-minimal_2.7.12-2_amd64.deb ... Unpacking python2.7-minimal (2.7.12-2) ... 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Unpacking python (2.7.11-2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../1-libpng16-16_1.6.24-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.24-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../2-libfreetype6_2.6.3-3+b1_amd64.deb ... Unpacking libfreetype6:amd64 (2.6.3-3+b1) ... Selecting previously unselected package ucf. Preparing to unpack .../3-ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../4-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../5-fontconfig-config_2.11.0-6.7_all.deb ... Unpacking fontconfig-config (2.11.0-6.7) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../6-libfontconfig1_2.11.0-6.7_amd64.deb ... Unpacking libfontconfig1:amd64 (2.11.0-6.7) ... Selecting previously unselected package fontconfig. Preparing to unpack .../7-fontconfig_2.11.0-6.7_amd64.deb ... Unpacking fontconfig (2.11.0-6.7) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../8-libsigsegv2_2.10-5_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-5) ... Setting up readline-common (6.3-8) ... Setting up libreadline6:amd64 (6.3-8+b4) ... Setting up libsigsegv2:amd64 (2.10-5) ... Selecting previously unselected package gawk. (Reading database ... 11414 files and directories currently installed.) Preparing to unpack .../00-gawk_1%3a4.1.3+dfsg-0.1_amd64.deb ... Unpacking gawk (1:4.1.3+dfsg-0.1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../01-libglib2.0-0_2.48.1-3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.48.1-3) ... Selecting previously unselected package libgts-0.7-5:amd64. 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Setting up libjbig0:amd64 (2.1-3.1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libbamtools2.4.0 (2.4.0+dfsg-6) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:amd64 (2.48.1-3) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-15) ... Setting up libdatrie1:amd64 (0.2.10-2) ... Setting up libtiff5:amd64 (4.0.6-2) ... Setting up gettext-base (0.19.8.1-1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up gawk (1:4.1.3+dfsg-0.1) ... Setting up libicu57:amd64 (57.1-3) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-1+b1) ... Setting up libfreetype6:amd64 (2.6.3-3+b1) ... Setting up libtasn1-6:amd64 (4.9-4) ... Setting up libmagic-mgc (1:5.28-4) ... Setting up libmagic1:amd64 (1:5.28-4) ... Setting up libhogweed4:amd64 (3.2-1) ... Setting up lsb-base (9.20160629) ... Setting up libgraphite2-3:amd64 (1.3.8-1) ... Setting up libcroco3:amd64 (0.6.11-1) ... Setting up libssl1.0.2:amd64 (1.0.2h-1) ... Setting up libpixman-1-0:amd64 (0.33.6-1) ... Setting up libssh2-1:amd64 (1.7.0-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libp11-kit0:amd64 (0.23.2-5) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up libsqlite3-0:amd64 (3.14.1-1) ... Setting up liblocale-gettext-perl (1.07-3) ... Setting up libthai-data (0.1.25-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.10) ... 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 x11-common (1:7.7+16) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libcdt5 (2.38.0-15) ... Setting up libx11-data (2:1.6.3-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.12-2) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-1) ... Setting up libidn11:amd64 (1.33-1) ... Setting up libcgraph6 (2.38.0-15) ... Setting up libwebp6:amd64 (0.5.1-2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libfile-stripnondeterminism-perl (0.023-2) ... Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-1.2) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up gettext (0.19.8.1-1) ... Setting up libgvpr2 (2.38.0-15) ... Setting up libbamtools-dev (2.4.0+dfsg-6) ... Setting up libgnutls30:amd64 (3.5.3-3) ... Setting up python2.7 (2.7.12-2) ... Setting up libharfbuzz0b:amd64 (1.2.7-1+b1) ... Setting up autoconf (2.69-10) ... Setting up libthai0:amd64 (0.1.25-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ... Setting up file (1:5.28-4) ... Setting up libkrb5support0:amd64 (1.14.3+dfsg-1) ... Setting up libpython-stdlib:amd64 (2.7.11-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ... Setting up automake (1:1.15-4) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.4) ... Setting up libice6:amd64 (2:1.0.9-1+b1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxcb1:amd64 (1.11.1-1.1) ... Setting up python (2.7.11-2) ... Setting up libtool (2.4.6-2) ... Setting up libfontconfig1:amd64 (2.11.0-6.7) ... Setting up libsm6:amd64 (2:1.2.2-1+b1) ... Setting up libk5crypto3:amd64 (1.14.3+dfsg-1) ... Setting up libxcb-render0:amd64 (1.11.1-1.1) ... Setting up po-debconf (1.0.19) ... Setting up libx11-6:amd64 (2:1.6.3-1) ... Setting up libxcb-shm0:amd64 (1.11.1-1.1) ... Setting up libxpm4:amd64 (1:3.5.11-1+b1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.9-2) ... Setting up libkrb5-3:amd64 (1.14.3+dfsg-1) ... Setting up fontconfig (2.11.0-6.7) ... Regenerating fonts cache... done. Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libgd3:amd64 (2.2.3-3+b1) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.14.3+dfsg-1) ... Setting up libpango-1.0-0:amd64 (1.40.1-1) ... Setting up libxaw7:amd64 (2:1.0.13-1) ... Setting up libcairo2:amd64 (1.14.6-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.50.1-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.1-1) ... Setting up libhts1:amd64 (1.3.1-2) ... Setting up python-pysam (0.9.1.4+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.1-1) ... Setting up samtools (1.3.1-2) ... Setting up libgvc6 (2.38.0-15) ... Setting up graphviz (2.38.0-15) ... Setting up python-ruffus (2.6.3+dfsg-4) ... Setting up dh-strip-nondeterminism (0.023-2) ... Setting up debhelper (9.20160814) ... Setting up dh-autoreconf (12) ... Setting up sbuild-build-depends-sga-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-5) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.27-6 dpkg-dev_1.18.10 g++-6_6.2.0-1 gcc-6_6.2.0-1 libc6-dev_2.23-5 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 linux-libc-dev_4.7.2-1 Package versions: adduser_3.115 apt_1.3~rc2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6 base-passwd_3.5.40 bash_4.3-15 binutils_2.27-6 bsdmainutils_9.0.10 bsdutils_1:2.28.1-1 build-essential_12.2 bzip2_1.0.6-8 clang-3.8_1:3.8.1-9 coreutils_8.25-2 cpp_4:6.1.1-1 cpp-6_6.2.0-1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debian-archive-keyring_2014.3 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 eatmydata_105-3 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 g++_4:6.1.1-1 g++-6_6.2.0-1 gawk_1:4.1.3+dfsg-0.1 gcc_4:6.1.1-1 gcc-6_6.2.0-1 gcc-6-base_6.2.0-1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gpgv_2.1.14-5 graphviz_2.38.0-15 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init-system-helpers_1.42 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapt-pkg5.0_1.3~rc2 libarchive-zip-perl_1.59-1 libasan3_6.2.0-1 libatomic1_6.2.0-1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libbamtools-dev_2.4.0+dfsg-6 libbamtools2.4.0_2.4.0+dfsg-6 libblkid1_2.28.1-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-5 libc-dev-bin_2.23-5 libc6_2.23-5 libc6-dev_2.23-5 libcairo2_1.14.6-1+b1 libcap-ng0_0.7.7-3 libcc1-0_6.2.0-1 libcdt5_2.38.0-15 libcgraph6_2.38.0-15 libcilkrts5_6.2.0-1 libclang-common-3.8-dev_1:3.8.1-9 libclang1-3.8_1:3.8.1-9 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcurl3-gnutls_7.50.1-1 libdatrie1_0.2.10-2 libdb5.3_5.3.28-12 libdebconfclient0_0.215 libdpkg-perl_1.18.10 libeatmydata1_105-3 libedit2_3.1-20150325-1+b1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libfontconfig1_2.11.0-6.7 libfreetype6_2.6.3-3+b1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-1 libgcc1_1:6.2.0-1 libgcrypt20_1.7.3-1 libgd3_2.2.3-3+b1 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-3 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-3 libgomp1_6.2.0-1 libgpg-error0_1.24-1 libgraphite2-3_1.3.8-1 libgssapi-krb5-2_1.14.3+dfsg-1 libgts-0.7-5_0.7.6+darcs121130-1.2 libgvc6_2.38.0-15 libgvpr2_2.38.0-15 libharfbuzz0b_1.2.7-1+b1 libhogweed4_3.2-1 libhts1_1.3.1-2 libice6_2:1.0.9-1+b1 libicu57_57.1-3 libidn11_1.33-1 libisl15_0.17.1-1 libitm1_6.2.0-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.0-1 libk5crypto3_1.14.3+dfsg-1 libkeyutils1_1.5.9-9 libkrb5-3_1.14.3+dfsg-1 libkrb5support0_1.14.3+dfsg-1 libldap-2.4-2_2.4.42+dfsg-2+b2 libllvm3.8_1:3.8.1-9 liblocale-gettext-perl_1.07-3 liblsan0_6.2.0-1 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libmpx2_6.2.0-1 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libnettle6_3.2-1 libnghttp2-14_1.13.0-1 libobjc-6-dev_6.2.0-1 libobjc4_6.2.0-1 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpango-1.0-0_1.40.1-1 libpangocairo-1.0-0_1.40.1-1 libpangoft2-1.0-0_1.40.1-1 libpathplan4_2.38.0-15 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpng16-16_1.6.24-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-2 libpython2.7-stdlib_2.7.12-2 libquadmath0_6.2.0-1 libreadline6_6.3-8+b4 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28.1-1 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.14.1-1 libss2_1.43.1-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2h-1 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 libsystemd0_231-5 libtasn1-6_4.9-4 libthai-data_0.1.25-1 libthai0_0.1.25-1 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libtsan0_6.2.0-1 libubsan0_6.2.0-1 libudev1_231-5 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-5 libuuid1_2.28.1-1 libwebp6_0.5.1-2 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.11.1-1.1 libxcb-shm0_1.11.1-1.1 libxcb1_1.11.1-1.1 libxdmcp6_1:1.1.2-1.1 libxdot4_2.38.0-15 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-1+b1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrender1_1:0.9.9-2 libxt6_1:1.1.5-1 linux-libc-dev_4.7.2-1 login_1:4.2-3.1 lsb-base_9.20160629 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28.1-1 multiarch-support_2.23-5 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 python_2.7.11-2 python-minimal_2.7.11-2 python-pysam_0.9.1.4+ds-1 python-ruffus_2.6.3+dfsg-4 python2.7_2.7.12-2 python2.7-minimal_2.7.12-2 readline-common_6.3-8 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-sga-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 ucf_3.0036 util-linux_2.28.1-1 x11-common_1:7.7+16 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 +------------------------------------------------------------------------------+ | 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 Jul 23 07:24:10 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./sga_0.10.14-3.dsc dpkg-source: info: extracting sga in /<> dpkg-source: info: unpacking sga_0.10.14.orig.tar.gz dpkg-source: info: unpacking sga_0.10.14-3.debian.tar.xz dpkg-source: info: applying 0002-no-rpath.patch dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch dpkg-source: info: applying 0006-remove-google-addsense.patch dpkg-source: info: applying 0007-gcc-6.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-ca2d9914-846f-4973-a3a1-714ed5b4dc33 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package sga dpkg-buildpackage: info: source version 0.10.14-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Afif Elghraoui dpkg-source --before-build sga-0.10.14 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src --parallel --with autoreconf dh_testdir -O--sourcedirectory=src -O--parallel dh_auto_clean -O--sourcedirectory=src -O--parallel dh_autoreconf_clean -O--sourcedirectory=src -O--parallel dh_clean -O--sourcedirectory=src -O--parallel debian/rules build-arch dh build-arch --sourcedirectory=src --parallel --with autoreconf dh_testdir -a -O--sourcedirectory=src -O--parallel dh_update_autotools_config -a -O--sourcedirectory=src -O--parallel dh_autoreconf -a -O--sourcedirectory=src -O--parallel configure.ac:12: installing './compile' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Algorithm/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --with-bamtools=/usr/ ./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 --with-bamtools=/usr/ configure: WARNING: unrecognized options: --disable-maintainer-mode 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... gawk 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 for ranlib... ranlib checking how to run the C++ preprocessor... g++ -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 zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing clock_gettime... none required checking for OpenMP flag of C++ compiler... unknown checking for host type... you are not using osx so multi-threading should work. checking google/sparse_hash_set usability... yes checking google/sparse_hash_set presence... yes checking for google/sparse_hash_set... yes checking for google/sparse_hash_set... (cached) yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... no checking unordered_map presence... no checking for unordered_map... no checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking unordered_set usability... no checking unordered_set presence... no checking for unordered_set... no checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/hash_set... yes checking api/BamReader.h usability... yes checking api/BamReader.h presence... yes checking for api/BamReader.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating Thirdparty/Makefile config.status: creating Util/Makefile config.status: creating SQG/Makefile config.status: creating Bigraph/Makefile config.status: creating Algorithm/Makefile config.status: creating StringGraph/Makefile config.status: creating Concurrency/Makefile config.status: creating SuffixTools/Makefile config.status: creating GraphDiff/Makefile config.status: creating Scaffold/Makefile config.status: creating SGA/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/<>' dh_auto_build -a -O--sourcedirectory=src -O--parallel make -j1 make[1]: Entering directory '/<>/src' make all-recursive make[2]: Entering directory '/<>/src' Making all in bin make[3]: Entering directory '/<>/src/bin' cp -n sga-bam2de.pl sga-bam2de cp -n sga-mergeDriver.pl sga-mergeDriver make[3]: Leaving directory '/<>/src/bin' Making all in Thirdparty make[3]: Entering directory '/<>/src/Thirdparty' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o gzstream.o gzstream.C gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -O3 -c -o stdaln.o stdaln.c g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o overlapper.o overlapper.cpp overlapper.cpp:37:64: warning: missing field 'gap_s1_start' initializer [-Wmissing-field-initializers] OverlapperParams default_params = { 2, -6, -3, -2, ALT_OVERLAP }; ^ overlapper.cpp:38:69: warning: missing field 'gap_s1_start' initializer [-Wmissing-field-initializers] OverlapperParams ungapped_params = { 2, -10000, -3, -2, ALT_OVERLAP }; ^ overlapper.cpp:635:22: warning: unused variable 'FROM_INVALID' [-Wunused-const-variable] static const uint8_t FROM_INVALID = 3; ^ 3 warnings generated. g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o multiple_alignment.o multiple_alignment.cpp gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -O3 -c -o bcr.o bcr.c bcr.c:189:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(ld->a[i], 8, x, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~ bcr.c:186:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&x, sizeof(int), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~ bcr.c:183:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&ld->max, sizeof(int), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:461:64: warning: while loop has empty body [-Wempty-body] static void *worker(void *data) { while (worker_aux(data) == 0); return 0; } ^ bcr.c:461:64: note: put the semicolon on a separate line to silence this warning 4 warnings generated. g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o MurmurHash3.o MurmurHash3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o count_min_sketch.o count_min_sketch.cpp rm -f libthirdparty.a ar cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libthirdparty.a make[3]: Leaving directory '/<>/src/Thirdparty' Making all in Util make[3]: Entering directory '/<>/src/Util' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Util.o `test -f 'Util.cpp' || echo './'`Util.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Alphabet.o `test -f 'Alphabet.cpp' || echo './'`Alphabet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Contig.o `test -f 'Contig.cpp' || echo './'`Contig.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-ReadInfoTable.o `test -f 'ReadInfoTable.cpp' || echo './'`ReadInfoTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-SeqReader.o `test -f 'SeqReader.cpp' || echo './'`SeqReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-DNAString.o `test -f 'DNAString.cpp' || echo './'`DNAString.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Match.o `test -f 'Match.cpp' || echo './'`Match.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Pileup.o `test -f 'Pileup.cpp' || echo './'`Pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-BitChar.o `test -f 'BitChar.cpp' || echo './'`BitChar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Interval.o `test -f 'Interval.cpp' || echo './'`Interval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-SeqCoord.o `test -f 'SeqCoord.cpp' || echo './'`SeqCoord.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-MultiOverlap.o `test -f 'MultiOverlap.cpp' || echo './'`MultiOverlap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-QualityVector.o `test -f 'QualityVector.cpp' || echo './'`QualityVector.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-PrimerScreen.o `test -f 'PrimerScreen.cpp' || echo './'`PrimerScreen.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-CorrectionThresholds.o `test -f 'CorrectionThresholds.cpp' || echo './'`CorrectionThresholds.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-StdAlnTools.o `test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-QualityTable.o `test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp rm -f libutil.a ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libutil.a make[3]: Leaving directory '/<>/src/Util' Making all in SQG make[3]: Entering directory '/<>/src/SQG' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsqg_a-SQG.o `test -f 'SQG.cpp' || echo './'`SQG.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp rm -f libsqg.a ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsqg.a make[3]: Leaving directory '/<>/src/SQG' Making all in Bigraph make[3]: Entering directory '/<>/src/Bigraph' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libbigraph_a-Bigraph.o `test -f 'Bigraph.cpp' || echo './'`Bigraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libbigraph_a-Vertex.o `test -f 'Vertex.cpp' || echo './'`Vertex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libbigraph_a-Edge.o `test -f 'Edge.cpp' || echo './'`Edge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp rm -f libbigraph.a ar cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libbigraph.a make[3]: Leaving directory '/<>/src/Bigraph' Making all in Algorithm make[3]: Entering directory '/<>/src/Algorithm' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-OverlapAlgorithm.o `test -f 'OverlapAlgorithm.cpp' || echo './'`OverlapAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-SearchSeed.o `test -f 'SearchSeed.cpp' || echo './'`SearchSeed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-OverlapBlock.o `test -f 'OverlapBlock.cpp' || echo './'`OverlapBlock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-SearchHistory.o `test -f 'SearchHistory.cpp' || echo './'`SearchHistory.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-ErrorCorrectProcess.o `test -f 'ErrorCorrectProcess.cpp' || echo './'`ErrorCorrectProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-OverlapTools.o `test -f 'OverlapTools.cpp' || echo './'`OverlapTools.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp In file included from ConnectProcess.cpp:10: ./ConnectProcess.h:10:9: warning: 'CONNECTROCESS_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef CONNECTROCESS_H ^~~~~~~~~~~~~~~ ./ConnectProcess.h:11:9: note: 'CONNECTPROCESS_H' is defined here; did you mean 'CONNECTROCESS_H'? #define CONNECTPROCESS_H ^~~~~~~~~~~~~~~~ CONNECTROCESS_H 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-StringGraphGenerator.o `test -f 'StringGraphGenerator.cpp' || echo './'`StringGraphGenerator.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-FMMergeProcess.o `test -f 'FMMergeProcess.cpp' || echo './'`FMMergeProcess.cpp In file included from FMMergeProcess.cpp:9: ./FMMergeProcess.h:88:20: warning: private field 'm_pMarkedReads' is not used [-Wunused-private-field] BitVector* m_pMarkedReads; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-StatsProcess.o `test -f 'StatsProcess.cpp' || echo './'`StatsProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.cpp In file included from ClusterProcess.cpp:9: ./ClusterProcess.h:73:20: warning: private field 'm_pMarkedReads' is not used [-Wunused-private-field] BitVector* m_pMarkedReads; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-ReadCluster.o `test -f 'ReadCluster.cpp' || echo './'`ReadCluster.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp In file included from StringThreader.cpp:14: ./StringThreader.h:147:28: warning: private field 'm_pQuery' is not used [-Wunused-private-field] const std::string* m_pQuery; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp ExtensionDP.cpp:22:18: warning: unused variable 'MINUS_INF' [-Wunused-const-variable] static const int MINUS_INF = -1073741823; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-HaplotypeBuilder.o `test -f 'HaplotypeBuilder.cpp' || echo './'`HaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp rm -f libalgorithm.a ar cru libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalgorithm.a make[3]: Leaving directory '/<>/src/Algorithm' Making all in StringGraph make[3]: Entering directory '/<>/src/StringGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-SGUtil.o `test -f 'SGUtil.cpp' || echo './'`SGUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-SGAlgorithms.o `test -f 'SGAlgorithms.cpp' || echo './'`SGAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-SGVisitors.o `test -f 'SGVisitors.cpp' || echo './'`SGVisitors.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-CompleteOverlapSet.o `test -f 'CompleteOverlapSet.cpp' || echo './'`CompleteOverlapSet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-RemovalAlgorithm.o `test -f 'RemovalAlgorithm.cpp' || echo './'`RemovalAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-SGSearch.o `test -f 'SGSearch.cpp' || echo './'`SGSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libstringgraph_a-SGWalk.o `test -f 'SGWalk.cpp' || echo './'`SGWalk.cpp rm -f libstringgraph.a ar cru libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libstringgraph.a make[3]: Leaving directory '/<>/src/StringGraph' Making all in Concurrency make[3]: Entering directory '/<>/src/Concurrency' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libconcurrency_a-OverlapProcess.o `test -f 'OverlapProcess.cpp' || echo './'`OverlapProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp rm -f libconcurrency.a ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libconcurrency.a make[3]: Leaving directory '/<>/src/Concurrency' Making all in SuffixTools make[3]: Entering directory '/<>/src/SuffixTools' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-STCommon.o `test -f 'STCommon.cpp' || echo './'`STCommon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-Occurrence.o `test -f 'Occurrence.cpp' || echo './'`Occurrence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SuffixArray.o `test -f 'SuffixArray.cpp' || echo './'`SuffixArray.cpp In file included from SuffixArray.cpp:10: ./InverseSuffixArray.h:10:9: warning: 'INVERSESUFFIXARRAY_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef INVERSESUFFIXARRAY_H ^~~~~~~~~~~~~~~~~~~~ ./InverseSuffixArray.h:11:9: note: 'INVERSESUFFIXARRAH_H' is defined here; did you mean 'INVERSESUFFIXARRAY_H'? #define INVERSESUFFIXARRAH_H ^~~~~~~~~~~~~~~~~~~~ INVERSESUFFIXARRAY_H 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SuffixCompare.o `test -f 'SuffixCompare.cpp' || echo './'`SuffixCompare.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-InverseSuffixArray.o `test -f 'InverseSuffixArray.cpp' || echo './'`InverseSuffixArray.cpp In file included from InverseSuffixArray.cpp:10: ./InverseSuffixArray.h:10:9: warning: 'INVERSESUFFIXARRAY_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef INVERSESUFFIXARRAY_H ^~~~~~~~~~~~~~~~~~~~ ./InverseSuffixArray.h:11:9: note: 'INVERSESUFFIXARRAH_H' is defined here; did you mean 'INVERSESUFFIXARRAY_H'? #define INVERSESUFFIXARRAH_H ^~~~~~~~~~~~~~~~~~~~ INVERSESUFFIXARRAY_H 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SACAInducedCopying.o `test -f 'SACAInducedCopying.cpp' || echo './'`SACAInducedCopying.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTWriter.o `test -f 'BWTWriter.cpp' || echo './'`BWTWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SAReader.o `test -f 'SAReader.cpp' || echo './'`SAReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SAWriter.o `test -f 'SAWriter.cpp' || echo './'`SAWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-RankProcess.o `test -f 'RankProcess.cpp' || echo './'`RankProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTWriterAscii.o `test -f 'BWTWriterAscii.cpp' || echo './'`BWTWriterAscii.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTReaderAscii.o `test -f 'BWTReaderAscii.cpp' || echo './'`BWTReaderAscii.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTIntervalCache.o `test -f 'BWTIntervalCache.cpp' || echo './'`BWTIntervalCache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-QuickBWT.o `test -f 'QuickBWT.cpp' || echo './'`QuickBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-SampledSuffixArray.o `test -f 'SampledSuffixArray.cpp' || echo './'`SampledSuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTCABauerCoxRosone.o `test -f 'BWTCABauerCoxRosone.cpp' || echo './'`BWTCABauerCoxRosone.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-BWTCARopebwt.o `test -f 'BWTCARopebwt.cpp' || echo './'`BWTCARopebwt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp rm -f libsuffixtools.a ar cru libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsuffixtools.a make[3]: Leaving directory '/<>/src/SuffixTools' Making all in Scaffold make[3]: Entering directory '/<>/src/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldVertex.o `test -f 'ScaffoldVertex.cpp' || echo './'`ScaffoldVertex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldEdge.o `test -f 'ScaffoldEdge.cpp' || echo './'`ScaffoldEdge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldGraph.o `test -f 'ScaffoldGraph.cpp' || echo './'`ScaffoldGraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldVisitors.o `test -f 'ScaffoldVisitors.cpp' || echo './'`ScaffoldVisitors.cpp In file included from ScaffoldVisitors.cpp:10: ./ScaffoldVisitors.h:76:16: warning: private field 'm_threshold' is not used [-Wunused-private-field] double m_threshold; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldLink.o `test -f 'ScaffoldLink.cpp' || echo './'`ScaffoldLink.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldRecord.o `test -f 'ScaffoldRecord.cpp' || echo './'`ScaffoldRecord.cpp In file included from ScaffoldRecord.cpp:11: ./ScaffoldRecord.h:117:23: warning: private field 'm_pStats' is not used [-Wunused-private-field] ResolveStats* m_pStats; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldGroup.o `test -f 'ScaffoldGroup.cpp' || echo './'`ScaffoldGroup.cpp In file included from ScaffoldGroup.cpp:10: ./ScaffoldGroup.h:68:31: warning: private field 'm_pRootVertex' is not used [-Wunused-private-field] const ScaffoldVertex* m_pRootVertex; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldAlgorithms.o `test -f 'ScaffoldAlgorithms.cpp' || echo './'`ScaffoldAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libscaffold_a-ScaffoldSequenceCollection.o `test -f 'ScaffoldSequenceCollection.cpp' || echo './'`ScaffoldSequenceCollection.cpp rm -f libscaffold.a ar cru libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libscaffold.a make[3]: Leaving directory '/<>/src/Scaffold' Making all in GraphDiff make[3]: Entering directory '/<>/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-DindelUtil.o `test -f 'DindelUtil.cpp' || echo './'`DindelUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-DindelRealignWindow.o `test -f 'DindelRealignWindow.cpp' || echo './'`DindelRealignWindow.cpp In file included from DindelRealignWindow.cpp:32: ./DindelHMM.h:116:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DEBUGDINDELHMM && 1) ^ ~ ./DindelHMM.h:116:22: note: use '&' for a bitwise operation if (DEBUGDINDELHMM && 1) ^~ & ./DindelHMM.h:116:22: note: remove constant to silence this warning if (DEBUGDINDELHMM && 1) ~^~~~ ./DindelHMM.h:149:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DEBUGDINDELHMM && 1) ^ ~ ./DindelHMM.h:149:22: note: use '&' for a bitwise operation if (DEBUGDINDELHMM && 1) ^~ & ./DindelHMM.h:149:22: note: remove constant to silence this warning if (DEBUGDINDELHMM && 1) ~^~~~ DindelRealignWindow.cpp:394:22: warning: use of logical '||' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG || DINDEL_DEBUG_3) ^ ~~~~~~~~~~~~~~ DindelRealignWindow.cpp:394:22: note: use '|' for a bitwise operation if (DINDEL_DEBUG || DINDEL_DEBUG_3) ^~ | DindelRealignWindow.cpp:462:21: warning: use of logical '||' with constant operand [-Wconstant-logical-operand] if(DINDEL_DEBUG || verbose) ^ ~~~~~~~ DindelRealignWindow.cpp:462:21: note: use '|' for a bitwise operation if(DINDEL_DEBUG || verbose) ^~ | DindelRealignWindow.cpp:633:38: warning: use of logical '||' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG || 0) ^ ~ DindelRealignWindow.cpp:633:38: note: use '|' for a bitwise operation if (DINDEL_DEBUG || 0) ^~ | DindelRealignWindow.cpp:859:32: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG_3 && 0) ^ ~ DindelRealignWindow.cpp:859:32: note: use '&' for a bitwise operation if (DINDEL_DEBUG_3 && 0) ^~ & DindelRealignWindow.cpp:859:32: note: remove constant to silence this warning if (DINDEL_DEBUG_3 && 0) ~^~~~ DindelRealignWindow.cpp:1575:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG && DRHA) ^ ~~~~ DindelRealignWindow.cpp:1575:22: note: use '&' for a bitwise operation if (DINDEL_DEBUG && DRHA) ^~ & DindelRealignWindow.cpp:1575:22: note: remove constant to silence this warning if (DINDEL_DEBUG && DRHA) ~^~~~~~~ DindelRealignWindow.cpp:1601:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG && DRHA) ^ ~~~~ DindelRealignWindow.cpp:1601:22: note: use '&' for a bitwise operation if (DINDEL_DEBUG && DRHA) ^~ & DindelRealignWindow.cpp:1601:22: note: remove constant to silence this warning if (DINDEL_DEBUG && DRHA) ~^~~~~~~ DindelRealignWindow.cpp:1697:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG && DRHA) ^ ~~~~ DindelRealignWindow.cpp:1697:22: note: use '&' for a bitwise operation if (DINDEL_DEBUG && DRHA) ^~ & DindelRealignWindow.cpp:1697:22: note: remove constant to silence this warning if (DINDEL_DEBUG && DRHA) ~^~~~~~~ DindelRealignWindow.cpp:1701:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG && DRHA) ^ ~~~~ DindelRealignWindow.cpp:1701:22: note: use '&' for a bitwise operation if (DINDEL_DEBUG && DRHA) ^~ & DindelRealignWindow.cpp:1701:22: note: remove constant to silence this warning if (DINDEL_DEBUG && DRHA) ~^~~~~~~ DindelRealignWindow.cpp:2234:23: warning: use of logical '||' with constant operand [-Wconstant-logical-operand] if(DINDEL_DEBUG_3 || SHOWHAPFREQ) ^ ~~~~~~~~~~~ DindelRealignWindow.cpp:2234:23: note: use '|' for a bitwise operation if(DINDEL_DEBUG_3 || SHOWHAPFREQ) ^~ | DindelRealignWindow.cpp:2372:23: warning: use of logical '||' with constant operand [-Wconstant-logical-operand] if(DINDEL_DEBUG_3 || SHOWHAPFREQ) ^ ~~~~~~~~~~~ DindelRealignWindow.cpp:2372:23: note: use '|' for a bitwise operation if(DINDEL_DEBUG_3 || SHOWHAPFREQ) ^~ | DindelRealignWindow.cpp:2694:56: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG_3 && 0) ^ ~ DindelRealignWindow.cpp:2694:56: note: use '&' for a bitwise operation if (DINDEL_DEBUG_3 && 0) ^~ & DindelRealignWindow.cpp:2694:56: note: remove constant to silence this warning if (DINDEL_DEBUG_3 && 0) ~^~~~ DindelRealignWindow.cpp:4474:40: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DINDEL_DEBUG_3 && 0) ^ ~ DindelRealignWindow.cpp:4474:40: note: use '&' for a bitwise operation if (DINDEL_DEBUG_3 && 0) ^~ & DindelRealignWindow.cpp:4474:40: note: remove constant to silence this warning if (DINDEL_DEBUG_3 && 0) ~^~~~ DindelRealignWindow.cpp:43:11: warning: unused variable 'ALWAYS_REALIGN' [-Wunused-const-variable] const int ALWAYS_REALIGN=1; ^ DindelRealignWindow.cpp:47:11: warning: unused variable 'REPOSITIONVARIANTSSLOW' [-Wunused-const-variable] const int REPOSITIONVARIANTSSLOW=0; // uses slow code to reposition indels. ^ 16 warnings generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-DindelHMM.o `test -f 'DindelHMM.cpp' || echo './'`DindelHMM.cpp In file included from DindelHMM.cpp:18: ./DindelHMM.h:116:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DEBUGDINDELHMM && 1) ^ ~ ./DindelHMM.h:116:22: note: use '&' for a bitwise operation if (DEBUGDINDELHMM && 1) ^~ & ./DindelHMM.h:116:22: note: remove constant to silence this warning if (DEBUGDINDELHMM && 1) ~^~~~ ./DindelHMM.h:149:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (DEBUGDINDELHMM && 1) ^ ~ ./DindelHMM.h:149:22: note: use '&' for a bitwise operation if (DEBUGDINDELHMM && 1) ^~ & ./DindelHMM.h:149:22: note: remove constant to silence this warning if (DEBUGDINDELHMM && 1) ~^~~~ 2 warnings generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-OverlapHaplotypeBuilder.o `test -f 'OverlapHaplotypeBuilder.cpp' || echo './'`OverlapHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-StringHaplotypeBuilder.o `test -f 'StringHaplotypeBuilder.cpp' || echo './'`StringHaplotypeBuilder.cpp In file included from StringHaplotypeBuilder.cpp:10: ./StringHaplotypeBuilder.h:80:16: warning: private field 'm_numReads' is not used [-Wunused-private-field] size_t m_numReads; ^ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.o `test -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'`DeBruijnHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-VCFTester.o `test -f 'VCFTester.cpp' || echo './'`VCFTester.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-GraphCompare.o `test -f 'GraphCompare.cpp' || echo './'`GraphCompare.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o `test -f 'OverlapExtractorWithCorrection.cpp' || echo './'`OverlapExtractorWithCorrection.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp rm -f libgraphdiff.a ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgraphdiff.a make[3]: Leaving directory '/<>/src/GraphDiff' Making all in SGA make[3]: Entering directory '/<>/src/SGA' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-sga.o `test -f 'sga.cpp' || echo './'`sga.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-index.o `test -f 'index.cpp' || echo './'`index.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-overlap.o `test -f 'overlap.cpp' || echo './'`overlap.cpp overlap.cpp:371:8: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!IS_POWER_OF_2(opt::sampleRate)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlap.cpp:371:8: note: add parentheses after the '!' to evaluate the comparison first if(!IS_POWER_OF_2(opt::sampleRate)) ^ ( ) overlap.cpp:371:8: note: add parentheses around left hand side expression to silence this warning 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-assemble.o `test -f 'assemble.cpp' || echo './'`assemble.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-correct.o `test -f 'correct.cpp' || echo './'`correct.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-oview.o `test -f 'oview.cpp' || echo './'`oview.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-preprocess.o `test -f 'preprocess.cpp' || echo './'`preprocess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-rmdup.o `test -f 'rmdup.cpp' || echo './'`rmdup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-merge.o `test -f 'merge.cpp' || echo './'`merge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-subgraph.o `test -f 'subgraph.cpp' || echo './'`subgraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-scaffold.o `test -f 'scaffold.cpp' || echo './'`scaffold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.cpp In file included from connect.cpp:26: ../Algorithm/ConnectProcess.h:10:9: warning: 'CONNECTROCESS_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef CONNECTROCESS_H ^~~~~~~~~~~~~~~ ../Algorithm/ConnectProcess.h:11:9: note: 'CONNECTPROCESS_H' is defined here; did you mean 'CONNECTROCESS_H'? #define CONNECTPROCESS_H ^~~~~~~~~~~~~~~~ CONNECTROCESS_H 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-walk.o `test -f 'walk.cpp' || echo './'`walk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-fm-merge.o `test -f 'fm-merge.cpp' || echo './'`fm-merge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-gmap.o `test -f 'gmap.cpp' || echo './'`gmap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-filterBAM.o `test -f 'filterBAM.cpp' || echo './'`filterBAM.cpp In file included from filterBAM.cpp:25: ../Algorithm/ConnectProcess.h:10:9: warning: 'CONNECTROCESS_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef CONNECTROCESS_H ^~~~~~~~~~~~~~~ ../Algorithm/ConnectProcess.h:11:9: note: 'CONNECTPROCESS_H' is defined here; did you mean 'CONNECTROCESS_H'? #define CONNECTPROCESS_H ^~~~~~~~~~~~~~~~ CONNECTROCESS_H 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-cluster.o `test -f 'cluster.cpp' || echo './'`cluster.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-graph-diff.o `test -f 'graph-diff.cpp' || echo './'`graph-diff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-graph-concordance.o `test -f 'graph-concordance.cpp' || echo './'`graph-concordance.cpp graph-concordance.cpp:214:12: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] if(end > chr.seq.length()) ~~~ ^ ~~~~~~~~~~~~~~~~ 1 warning generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-preqc.o `test -f 'preqc.cpp' || echo './'`preqc.cpp In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:170:3: warning: unused typedef 'StaticAssertTypedef170' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :105:1: note: expanded from here StaticAssertTypedef170 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:183:3: warning: unused typedef 'StaticAssertTypedef183' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :107:1: note: expanded from here StaticAssertTypedef183 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:189:3: warning: unused typedef 'StaticAssertTypedef189' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :109:1: note: expanded from here StaticAssertTypedef189 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:195:3: warning: unused typedef 'StaticAssertTypedef195' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :111:1: note: expanded from here StaticAssertTypedef195 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:219:3: warning: unused typedef 'StaticAssertTypedef219' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :115:1: note: expanded from here StaticAssertTypedef219 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:234:3: warning: unused typedef 'StaticAssertTypedef234' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :123:1: note: expanded from here StaticAssertTypedef234 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:252:3: warning: unused typedef 'StaticAssertTypedef252' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :125:1: note: expanded from here StaticAssertTypedef252 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:253:3: warning: unused typedef 'StaticAssertTypedef253' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :127:1: note: expanded from here StaticAssertTypedef253 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:271:3: warning: unused typedef 'StaticAssertTypedef271' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :129:1: note: expanded from here StaticAssertTypedef271 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:278:3: warning: unused typedef 'StaticAssertTypedef278' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :131:1: note: expanded from here StaticAssertTypedef278 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:286:3: warning: unused typedef 'StaticAssertTypedef286' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :133:1: note: expanded from here StaticAssertTypedef286 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:292:3: warning: unused typedef 'StaticAssertTypedef292' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :135:1: note: expanded from here StaticAssertTypedef292 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:303:3: warning: unused typedef 'StaticAssertTypedef303' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :137:1: note: expanded from here StaticAssertTypedef303 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:310:3: warning: unused typedef 'StaticAssertTypedef310' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :139:1: note: expanded from here StaticAssertTypedef310 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:318:3: warning: unused typedef 'StaticAssertTypedef318' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :141:1: note: expanded from here StaticAssertTypedef318 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:324:3: warning: unused typedef 'StaticAssertTypedef324' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :143:1: note: expanded from here StaticAssertTypedef324 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:348:3: warning: unused typedef 'StaticAssertTypedef348' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 4); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :147:1: note: expanded from here StaticAssertTypedef348 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:355:3: warning: unused typedef 'StaticAssertTypedef355' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :152:1: note: expanded from here StaticAssertTypedef355 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:363:3: warning: unused typedef 'StaticAssertTypedef363' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :154:1: note: expanded from here StaticAssertTypedef363 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:375:3: warning: unused typedef 'StaticAssertTypedef375' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :156:1: note: expanded from here StaticAssertTypedef375 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:382:3: warning: unused typedef 'StaticAssertTypedef382' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :158:1: note: expanded from here StaticAssertTypedef382 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:392:3: warning: unused typedef 'StaticAssertTypedef392' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :160:1: note: expanded from here StaticAssertTypedef392 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:398:3: warning: unused typedef 'StaticAssertTypedef398' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :162:1: note: expanded from here StaticAssertTypedef398 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:411:3: warning: unused typedef 'StaticAssertTypedef411' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :164:1: note: expanded from here StaticAssertTypedef411 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:418:3: warning: unused typedef 'StaticAssertTypedef418' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :166:1: note: expanded from here StaticAssertTypedef418 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:428:3: warning: unused typedef 'StaticAssertTypedef428' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :168:1: note: expanded from here StaticAssertTypedef428 ^ In file included from preqc.cpp:27: In file included from ../Thirdparty/rapidjson/document.h:4: In file included from ../Thirdparty/rapidjson/reader.h:7: In file included from ../Thirdparty/rapidjson/rapidjson.h:129: ../Thirdparty/rapidjson/encodings.h:434:3: warning: unused typedef 'StaticAssertTypedef434' [-Wunused-local-typedef] RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); ^ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: expanded from macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: expanded from macro 'RAPIDJSON_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:110:33: note: expanded from macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_DO_JOIN(X, Y) RAPIDJSON_DO_JOIN2(X, Y) ^ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: expanded from macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ :170:1: note: expanded from here StaticAssertTypedef434 ^ 27 warnings generated. g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o sga-overlap-long.o `test -f 'overlap-long.cpp' || echo './'`overlap-long.cpp overlap-long.cpp:202:5: error: use of undeclared identifier 'omp_set_num_threads' omp_set_num_threads(opt::numThreads); ^ overlap-long.cpp:380:8: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!IS_POWER_OF_2(opt::sampleRate)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlap-long.cpp:380:8: note: add parentheses after the '!' to evaluate the comparison first if(!IS_POWER_OF_2(opt::sampleRate)) ^ ( ) overlap-long.cpp:380:8: note: add parentheses around left hand side expression to silence this warning 1 warning and 1 error generated. Makefile:876: recipe for target 'sga-overlap-long.o' failed make[3]: *** [sga-overlap-long.o] Error 1 make[3]: Leaving directory '/<>/src/SGA' Makefile:359: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/<>/src' Makefile:300: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/<>/src' dh_auto_build: make -j1 returned exit code 2 debian/rules:12: 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 2016-08-29T17:01:51Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 0 Build-Time: 128 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 17 Job: sga_0.10.14-3 Machine Architecture: amd64 Package: sga Package-Time: 172 Source-Version: 0.10.14-3 Space: 0 Status: failed Version: 0.10.14-3 -------------------------------------------------------------------------------- Finished at 2016-08-29T17:01:51Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 172.875804457s