DC-Build-Header: ncbi-blast+ 2.4.0-3 / 2016-08-29 15:27:45 +0000 DC-Task: type:rebuild-binarch-only source:ncbi-blast+ version:2.4.0-3 chroot:unstable esttime:2301 logfile:/tmp/ncbi-blast+_2.4.0-3_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 ncbi-blast+_2.4.0-3' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-11-117.eu-central-1.compute.internal +==============================================================================+ | ncbi-blast+ 2.4.0-3 (amd64) Mon, 29 Aug 2016 15:27:45 +0000 | +==============================================================================+ Package: ncbi-blast+ Version: 2.4.0-3 Source Version: 2.4.0-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-043e44be-6e3b-43a2-bcb7-cd5abded77b6' 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 2s (1924 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 1s (21.5 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/ncbi-blast+-QriueX + 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 (69.4 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: 'ncbi-blast+' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/ncbi-blast+.git Please use: git clone https://anonscm.debian.org/git/debian-med/ncbi-blast+.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.0 MB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main ncbi-blast+ 2.4.0-3 (dsc) [2226 B] Get:2 http://127.0.0.1:9999/debian unstable/main ncbi-blast+ 2.4.0-3 (tar) [18.9 MB] Get:3 http://127.0.0.1:9999/debian unstable/main ncbi-blast+ 2.4.0-3 (diff) [28.4 kB] Fetched 19.0 MB in 0s (46.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' with '<>' I: NOTICE: Log filtering will replace 'build/ncbi-blast+-QriueX' 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 '/build/ncbi-blast+-QriueX/resolver-Y6HoWU/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:/build/ncbi-blast+-QriueX/resolver-Y6HoWU/apt_archive ./ InRelease Get:2 copy:/build/ncbi-blast+-QriueX/resolver-Y6HoWU/apt_archive ./ Release [957 B] Ign:3 copy:/build/ncbi-blast+-QriueX/resolver-Y6HoWU/apt_archive ./ Release.gpg Get:4 copy:/build/ncbi-blast+-QriueX/resolver-Y6HoWU/apt_archive ./ Sources [349 B] Get:5 copy:/build/ncbi-blast+-QriueX/resolver-Y6HoWU/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:/build/ncbi-blast+-QriueX/resolver-Y6HoWU/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 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: autotools-dev, debhelper (>= 9), libboost-test-dev, libbz2-dev, libc-dev-bin, libpcre3-dev, time, zlib1g-dev Filtered Build-Depends: autotools-dev, debhelper (>= 9), libboost-test-dev, libbz2-dev, libc-dev-bin, libpcre3-dev, time, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-ncbi-blast+-dummy' in '/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive/sbuild-build-depends-ncbi-blast+-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-ncbi-blast+-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive ./ InRelease Get:2 copy:/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive ./ Release [957 B] Ign:3 copy:/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive ./ Release.gpg Get:4 copy:/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive ./ Sources [394 B] Get:5 copy:/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive ./ Packages [481 B] Fetched 1832 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 ncbi-blast+ build dependencies (apt-based resolver) ----------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libboost-chrono1.61.0 libboost-system1.61.0 libboost-test-dev libboost-test1.61-dev libboost-test1.61.0 libboost-timer1.61.0 libboost1.61-dev libbz2-dev libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf time zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.61-doc libboost-atomic1.61-dev libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev libboost-date-time1.61-dev libboost-exception1.61-dev libboost-filesystem1.61-dev libboost-graph1.61-dev libboost-graph-parallel1.61-dev libboost-iostreams1.61-dev libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev libboost-program-options1.61-dev libboost-python1.61-dev libboost-random1.61-dev libboost-regex1.61-dev libboost-serialization1.61-dev libboost-signals1.61-dev libboost-system1.61-dev libboost-thread1.61-dev libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur bzip2-doc libglib2.0-data shared-mime-info xdg-user-dirs 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 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libboost-chrono1.61.0 libboost-system1.61.0 libboost-test-dev libboost-test1.61-dev libboost-test1.61.0 libboost-timer1.61.0 libboost1.61-dev libbz2-dev libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-ncbi-blast+-dummy time zlib1g-dev 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 28.8 MB of archives. After this operation, 189 MB of additional disk space will be used. Get:1 copy:/build/ncbi-blast+-QriueX/resolver-iyLKW6/apt_archive ./ sbuild-build-depends-ncbi-blast+-dummy 0.invalid.0 [828 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 libpcrecpp0v5 amd64 2:8.39-2 [151 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libboost-system1.61.0 amd64 1.61.0+dfsg-2.1 [32.1 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libboost-chrono1.61.0 amd64 1.61.0+dfsg-2.1 [35.8 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libboost1.61-dev amd64 1.61.0+dfsg-2.1 [6843 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libboost-timer1.61.0 amd64 1.61.0+dfsg-2.1 [34.2 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libboost-test1.61.0 amd64 1.61.0+dfsg-2.1 [226 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libboost-test1.61-dev amd64 1.61.0+dfsg-2.1 [262 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libboost-test-dev amd64 1.61.0.2 [3432 B] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libbz2-dev amd64 1.0.6-8 [29.0 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libpcre16-3 amd64 2:8.39-2 [258 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libpcre32-3 amd64 2:8.39-2 [248 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libpcre3-dev amd64 2:8.39-2 [645 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 time amd64 1.7-25.1 [31.0 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.8 MB in 0s (84.1 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 libpcrecpp0v5:amd64. Preparing to unpack .../04-libpcrecpp0v5_2%3a8.39-2_amd64.deb ... Unpacking libpcrecpp0v5:amd64 (2:8.39-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.28-4_amd64.deb ... Unpacking libmagic-mgc (1:5.28-4) ... 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Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:amd64 (57.1-3) ... Setting up libboost1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-1+b1) ... Setting up libmagic-mgc (1:5.28-4) ... Setting up libmagic1:amd64 (1:5.28-4) ... Setting up libcroco3:amd64 (0.6.11-1) ... 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 libboost-chrono1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up libpcrecpp0v5:amd64 (2:8.39-2) ... Setting up libpcre32-3:amd64 (2:8.39-2) ... Setting up libpcre16-3:amd64 (2:8.39-2) ... 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 autopoint (0.19.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libfile-stripnondeterminism-perl (0.023-2) ... Setting up libpcre3-dev:amd64 (2:8.39-2) ... Setting up gettext (0.19.8.1-1) ... Setting up libboost-timer1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.28-4) ... Setting up intltool-debian (0.35.0+20060710.4) ... 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 man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-test1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.19) ... Setting up libboost-test1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up libboost-test-dev:amd64 (1.61.0.2) ... Setting up dh-strip-nondeterminism (0.023-2) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160814) ... Setting up sbuild-build-depends-ncbi-blast+-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 g++_4:6.1.1-1 g++-6_6.2.0-1 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 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 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 libblkid1_2.28.1-1 libboost-chrono1.61.0_1.61.0+dfsg-2.1 libboost-system1.61.0_1.61.0+dfsg-2.1 libboost-test-dev_1.61.0.2 libboost-test1.61-dev_1.61.0+dfsg-2.1 libboost-test1.61.0_1.61.0+dfsg-2.1 libboost-timer1.61.0_1.61.0+dfsg-2.1 libboost1.61-dev_1.61.0+dfsg-2.1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.23-5 libc-dev-bin_2.23-5 libc6_2.23-5 libc6-dev_2.23-5 libcap-ng0_0.7.7-3 libcc1-0_6.2.0-1 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 libdb5.3_5.3.28-12 libdebconfclient0_0.215 libdpkg-perl_1.18.10 libeatmydata1_105-3 libedit2_3.1-20150325-1+b1 libfakeroot_1.21-1 libfdisk1_2.28.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-1 libgcc1_1:6.2.0-1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-3 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.2.0-1 libgpg-error0_1.24-1 libicu57_57.1-3 libisl15_0.17.1-1 libitm1_6.2.0-1 libllvm3.8_1:3.8.1-9 liblsan0_6.2.0-1 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 libobjc-6-dev_6.2.0-1 libobjc4_6.2.0-1 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 libpcre16-3_2:8.39-2 libpcre3_2:8.39-2 libpcre3-dev_2:8.39-2 libpcre32-3_2:8.39-2 libpcrecpp0v5_2:8.39-2 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libquadmath0_6.2.0-1 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.1-1 libss2_1.43.1-1 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 libsystemd0_231-5 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 libxml2_2.9.4+dfsg1-1+b1 linux-libc-dev_4.7.2-1 login_1:4.2-3.1 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17 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 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ncbi-blast+-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 time_1.7-25.1 util-linux_2.28.1-1 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 Aug 6 00:54:58 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ncbi-blast+_2.4.0-3.dsc dpkg-source: info: extracting ncbi-blast+ in /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0 dpkg-source: info: unpacking ncbi-blast+_2.4.0.orig.tar.gz dpkg-source: info: unpacking ncbi-blast+_2.4.0-3.debian.tar.xz dpkg-source: info: applying enable_clean_after_failed_compile dpkg-source: info: applying hurd_fixes dpkg-source: info: applying legacy_rename_rpsblast dpkg-source: info: applying fix_lib_deps dpkg-source: info: applying no_multiarch_rpath dpkg-source: info: applying use_pie_for_apps dpkg-source: info: applying skip_services_unit_test dpkg-source: info: applying fix_configure dpkg-source: info: applying fix_version_extraction dpkg-source: info: applying support_recent_boost dpkg-source: info: applying support_x32 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-043e44be-6e3b-43a2-bcb7-cd5abded77b6 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package ncbi-blast+ dpkg-buildpackage: info: source version 2.4.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Aaron M. Ucko dpkg-source --before-build ncbi-blast+-2.4.0 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean -Dc++ --with autotools_dev dh_testdir -O-Dc\+\+ dh_auto_clean -O-Dc\+\+ dh_autotools-dev_restoreconfig -O-Dc\+\+ debian/rules override_dh_clean make[1]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' cp c++/configure.orig configure.orig.save dh_clean #Tricky - for each module directory there may be several module files #or there may be none but then there is still a module named after the #directory. Clean everything! for x in c++/src/objects/* ; do \ (cd "$x" && ( \ mods="`echo *.module`" ; \ [ "${mods#*\*}" = "$mods" ] || mods="`basename $x`" ; \ for mod in $mods ; do \ ../../../BUILD/build/new_module.sh $mod purge_sources ; \ done ) ; \ ) ; \ done /bin/sh: 2: cd: can't cd to c++/src/objects/Makefile.in /bin/sh: 2: cd: can't cd to c++/src/objects/Makefile.sources /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 2: cd: can't cd to c++/src/objects/nt_sources.cmd /bin/sh: 2: cd: can't cd to c++/src/objects/nt_sources.sh /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found /bin/sh: 6: ../../../BUILD/build/new_module.sh: not found debian/rules:94: recipe for target 'override_dh_clean' failed make[1]: [override_dh_clean] Error 127 (ignored) rm -rf c++/compilers/dll c++/config.log c++/Makefile rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module find -name check_exec.pid -delete rm -rf c++/BUILD mv configure.orig.save c++/configure.orig make[1]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' debian/rules build-arch dh build-arch -Dc++ --with autotools_dev dh_testdir -a -O-Dc\+\+ dh_update_autotools_config -a -O-Dc\+\+ dh_autotools-dev_updateconfig -a -O-Dc\+\+ debian/rules override_dh_auto_configure make[1]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' cd c++ && LD_LIBRARY_PATH=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH} \ CONFIG_SHELL=/bin/bash ./configure --with-dll --with-mt --without-autodep --without-makefile-auto-update --with-flat-makefile --without-caution --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD --without-debug --without-downloaded-vdb --with-symbols CFLAGS_FOR_BUILD="-g -O2 -fdebug-prefix-map=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fPIE" LDFLAGS_FOR_BUILD="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--as-needed" configure: loading site script ./src/build-system/config.site configure: creating cache config.cache checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o 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 how to run the C preprocessor... gcc -E checking for gcc... gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes adjusted C compiler: /usr/bin/gcc adjusted C++ compiler: /usr/bin/g++ checking whether /usr/bin/gcc has an option to export all symbols... -Wl,-export-dynamic checking whether /usr/bin/gcc supports -Wl,--{en,dis}able-new-dtags... yes checking whether /usr/bin/g++ supports -stdlib=libc++... no checking whether _LIBCPP_VERSION is declared... no checking how to enable C++ '11 features in /usr/bin/g++ ... (cached) no checking how to enable C '11 or at least '99 features in /usr/bin/gcc ... 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(cached) yes checking size of size_t... 8 checking for amq... no checking whether /usr/bin/gcc supports -Wl,--no-allow-shlib-undefined... yes checking how to run the C preprocessor... gcc -E checking whether cross-directory hard links work... yes checking iostream usability... yes checking iostream presence... yes checking for iostream... yes checking iostream.h usability... no checking iostream.h presence... no checking for iostream.h... no checking fstream usability... yes checking fstream presence... yes checking for fstream... yes checking fstream.h usability... no checking fstream.h presence... no checking for fstream.h... no checking strstream usability... yes checking strstream presence... yes checking for strstream... yes checking strstream.h usability... no checking strstream.h presence... no checking for strstream.h... no checking strstrea.h usability... no checking strstrea.h presence... no checking for strstrea.h... no checking for inttypes.h... (cached) yes checking limits usability... yes checking limits presence... yes checking for limits... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for wstring... yes checking for socklen_t... yes checking atomic.h usability... no checking atomic.h presence... no checking for atomic.h... no checking cpuid.h usability... yes checking cpuid.h presence... yes checking for cpuid.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking ieeefp.h usability... no checking ieeefp.h presence... no checking for ieeefp.h... no checking poll.h usability... yes checking poll.h presence... yes checking for poll.h... yes checking sys/epoll.h usability... yes checking sys/epoll.h presence... yes checking for sys/epoll.h... yes checking sys/mount.h usability... yes checking sys/mount.h presence... yes checking for sys/mount.h... yes checking sys/sockio.h usability... no checking sys/sockio.h presence... no checking for sys/sockio.h... no checking sys/statvfs.h usability... yes checking sys/statvfs.h presence... yes checking for sys/statvfs.h... yes checking sys/sysinfo.h usability... yes checking sys/sysinfo.h presence... yes checking for sys/sysinfo.h... yes checking sys/vfs.h usability... yes checking sys/vfs.h presence... yes checking for sys/vfs.h... yes checking x86intrin.h usability... yes checking x86intrin.h presence... yes checking for x86intrin.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking libgen.h usability... yes checking libgen.h presence... yes checking for libgen.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking 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valgrind/memcheck.h presence... no checking for valgrind/memcheck.h... no checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking whether time.h and sys/time.h may both be included... yes checking for gethostbyname_r... 6 checking for gethostbyaddr_r... 8 checking for getservbyname_r... 6 checking for getpwuid_r... 5 checking for getlogin_r... yes checking for localtime_r... yes checking for pthread_setconcurrency... yes checking for pthread_atfork... yes checking return type of localtime_r... struct checking whether pthread mutexes are available... yes checking for vprintf... yes checking for _doprnt... no checking for alarm... yes checking for asprintf... yes checking for atoll... yes checking for basename... yes checking for euidaccess... yes checking for fseeko... yes checking for fstat... yes checking for getgrouplist... yes checking for getopt... yes checking for getpagesize... yes checking for getpass... yes checking for 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for struct tm.__tm_zone... no checking whether function prototypes can use throw(...)... yes checking for obsolete string::compare() syntax... no checking whether the auto_ptr template class works... yes checking for min/max templates... yes checking whether new C++ streams have ios_base::... yes checking for ios(_base)::register_callback... yes checking for std::char_traits::... yes checking for SysV semaphores... yes checking for union semun... no checking which way the stack grows... up checking whether the preprocessor supports C99-style variadic macros... yes checking whether the preprocessor supports GNU-style variadic macros... yes checking syntax for marking deprecated functions... __attribute__((__deprecated__)) checking how to force inlining... inline __attribute__((always_inline)) checking whether the C compiler supports __attribute__((destructor))... yes checking whether /usr/bin/gcc supports __attribute__((visibility("default")))... (cached) unnecessary checking whether the C compiler supports C99 restrict... __restrict__ checking whether the C++ compiler supports C99 restrict... __restrict__ checking syntax for marking functions that never return... __attribute__((__noreturn__)) checking syntax for marking functions whose result should be checked... __attribute__((warn_unused_result)) checking syntax for declaring thread-local variables... __thread checking syntax for marking types as packed to save memory... __attribute__((__packed__)) checking whether FIONBIO requires BSD_COMP to be defined... no checking whether INADDR_NONE is defined... yes checking whether unaligned reads are permissible... yes checking whether /usr/bin/gcc supports SIMD vector arithmetic... yes checking whether /usr/bin/gcc supports -funsafe-math-optimizations... yes checking whether /usr/bin/gcc supports -msse4.1... no checking whether /usr/bin/gcc supports -maes... yes checking whether /usr/bin/gcc supports -fdiagnostics-color=always... 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sched_yield... yes checking for library containing iconv... none required checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for libz... yes checking for libbz2... yes checking for libpcre... yes checking for libgmp... no checking for libgcrypt-config... no checking for libgcrypt... no checking for libhogweed... no checking for libgnutls-config... no checking for libgnutls... no checking for libssl... no checking for krb5-config... no checking for libgssapi_krb5... no checking for libcurl... no checking for reentrant Sybase libraries... no checking for Sybase... no checking for FreeTDS... no checking for mysql_config... no checking for Berkeley DB libraries... no checking for python... no checking for python2.5... no checking for python2.6... no checking for python2.7... no checking for python3... no checking for perl... /usr/bin/perl checking for usable Perl libraries... no checking Boost version... 1_61 configure: WARNING: Untested Boost version; may prove incompatible. configure: WARNING: If so, please re-run this script with the flag --without-boost. checking for Boost library name tag... -gcc42-mt-1_61-64 (autodetected) checking for Boost.Regex... no checking for Boost.Spirit... yes checking for Boost.System... no checking for Boost.Filesystem... no checking for Boost.Iostreams... no checking for Boost.Program-Options... no checking for Boost.Test... included-only checking for Boost.Thread... no checking for the NCBI C toolkit... no checking for X... no checking for XextCreateExtension in -lXext... no checking for XtMainLoop in -lXt... no checking for XmuMakeAtom in -lXmu... no checking for OpenGL... no checking for wx-config... no /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/build-system/configure: 1: ./configure.lineno: : Permission denied checking for wxWidgets... no checking for FastCGI libraries... no checking for FCGX_Accept_r... no checking for 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/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/winmask/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/dustmask/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/composition_adjustment/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/igblast/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/blastinput/unit_test/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/blastinput/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/core/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/api/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/format/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/unit_tests/seqdb_reader/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/unit_tests/api/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/unit_tests/blast_format/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/unit_tests/blastdb/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/unit_tests/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/dbindex/makeindex/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/dbindex/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/blast/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/segmask/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/algo/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/./Makefile config.status: creating /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/inc/ncbiconf_unix.h config.status: executing default commands /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib/ncbicfg.c is updated make[2]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/build-system/helpers' /usr/bin/make -f /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/Makefile.app.tmpl srcdir=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/build-system/helpers TMPL=run_with_lock -kw all make[3]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/build-system/helpers' gcc -c -g -O2 -fdebug-prefix-map=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fPIE /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/build-system/helpers/run_with_lock.c -o run_with_lock.o gcc -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--as-needed -fPIE -pie run_with_lock.o -Wl,-rpath,/usr/lib/ncbi-blast+ -Wl,-rpath-link,/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/lib -L/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/lib -lm -lpthread -o run_with_lock /bin/bash /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/scripts/common/impl/if_diff.sh /bin/ln -f run_with_lock /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/bin /bin/ln -f run_with_lock /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/bin/run_with_lock make[3]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/build-system/helpers' make[2]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/build-system/helpers' project_tree_builder is not found at /net/snowman/vol/export2/win-coremake/App/Ncbi/cppcore/ptb/Linux64/4.1.2/project_tree_builder Will build project_tree_builder locally ********************************************************************** Building project_tree_builder ********************************************************************** make[2]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' make[3]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' /usr/bin/make[3] (Makefile.precompile): Nothing to be done for `all'. make[3]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' /usr/bin/make[2] (Makefile.corelib.lib): Nothing to be done for `export-headers'. /usr/bin/make[2] (Makefile.test_mt.lib): Nothing to be done for `export-headers'. /usr/bin/make[2] (Makefile.test_boost.lib): Nothing to be done for `export-headers'. /usr/bin/make -f /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/Makefile.lib.tmpl srcdir=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/corelib TMPL=corelib -w all In file included from /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/corelib/ncbi_os_unix.cpp:33: In file included from /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/error_codes.hpp:38: /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1853:5: error: unknown type name 'unique_ptr' unique_ptr m_Properties; // Per-thread properties ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1853:15: error: expected member name or ';' after declaration specifiers unique_ptr m_Properties; // Per-thread properties ~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1854:5: error: unknown type name 'unique_ptr' unique_ptr m_DiagBuffer; // Thread's diag buffer ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1854:15: error: expected member name or ';' after declaration specifiers unique_ptr m_DiagBuffer; // Thread's diag buffer ~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1860:5: error: unknown type name 'unique_ptr' unique_ptr m_RequestCtx; // Request context ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1860:15: error: expected member name or ';' after declaration specifiers unique_ptr m_RequestCtx; // Request context ~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1861:5: error: unknown type name 'unique_ptr' unique_ptr m_DefaultRequestCtx; // Default request context ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1861:15: error: expected member name or ';' after declaration specifiers unique_ptr m_DefaultRequestCtx; // Default request context ~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:1820:48: error: use of undeclared identifier 'm_DiagBuffer' CDiagBuffer& GetDiagBuffer(void) { return *m_DiagBuffer; } ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2352:13: error: unknown type name 'unique_ptr' mutable unique_ptr m_Host; ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2352:23: error: expected member name or ';' after declaration specifiers mutable unique_ptr m_Host; ~~~~~~~~~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2354:5: error: unknown type name 'unique_ptr' unique_ptr m_Username; ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2354:15: error: expected member name or ';' after declaration specifiers unique_ptr m_Username; ~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2355:5: error: unknown type name 'unique_ptr' unique_ptr m_AppName; ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2355:15: error: expected member name or ';' after declaration specifiers unique_ptr m_AppName; ~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2357:13: error: unknown type name 'unique_ptr' mutable unique_ptr m_DefaultSessionId; ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2357:23: error: expected member name or ';' after declaration specifiers mutable unique_ptr m_DefaultSessionId; ~~~~~~~~~~~~~~~~~~^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2358:13: error: unknown type name 'unique_ptr' mutable unique_ptr m_DefaultHitId; ^ /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include/corelib/ncbidiag.hpp:2358:23: error: expected member name or ';' after declaration specifiers mutable unique_ptr m_DefaultHitId; ~~~~~~~~~~~~~~~~~~^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[3]: *** [ncbi_os_unix.o] Error 1 make[3]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' /usr/bin/g++ -c -Wall -Wno-format-y2k -pthread -g -O2 -fdebug-prefix-map=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/inc -I/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/include /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/corelib/ncbi_os_unix.cpp -o ncbi_os_unix.o /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/Makefile.rules:63: recipe for target 'ncbi_os_unix.o' failed make[3]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' FAILED: src/corelib/Makefile.corelib.lib make[3]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' /bin/rm -f libxncbi.so libxncbi.so .xncbi.dep .libxncbi.so.stamp /bin/rm -f /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/lib/libxncbi.so /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/status/.xncbi.dep make[3]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/src/build-system/Makefile.meta_l:271: recipe for target 'all.nonusr' failed make[2]: *** [all.nonusr] Error 2 make[2]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib' ------------------------------------------------------ Current dir: /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/corelib [create_flat_makefile.sh] FAILED (status 2): make =============================================================================== NCBI C++ Toolkit documentation: Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ Local: ./doc/public/index.html For the available configuration flags run: ./configure --help CFLAGS = -Wall -Wno-format-y2k -pthread -g -O2 -fdebug-prefix-map=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wno-deprecated-register -fPIC CXXFLAGS = -Wall -Wno-format-y2k -pthread -g -O2 -fdebug-prefix-map=/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-deprecated-register -fPIC CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -D_MT -D_REENTRANT -D_THREAD_SAFE LDFLAGS = -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--as-needed -g -O LIBRARIES: build as dynamic by default FEATURES: GCC MT LFS DLL DLL_BUILD unix WinMain Linux PACKAGES: enabled: Iconv Z BZ2 PCRE Boost.Spirit Boost.Test.Included disabled: UUID FUSE LocalZ LocalBZ2 LZO LocalPCRE GMP GCRYPT NETTLE GNUTLS OPENSSL KRB5 CURL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON PYTHON25 PYTHON26 PYTHON27 PYTHON3 PERL Boost.Filesystem Boost.Iostreams Boost.Program-Options Boost.Regex Boost.System Boost.Test Boost.Thread C-Toolkit OpenGL MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXML LIBXSLT LIBEXSLT Xerces Xalan Zorba SQLITE3 SQLITE3ASYNC VDB OECHEM SGE MUPARSER HDF5 JPEG PNG TIFF UNGIF GIF XPM FreeType FTGL MAGIC MIMETIC GSOAP AVRO Cereal SASL2 MONGODB GMOCK PROJECTS: enabled: cgi serial objects app algo disabled: local_lbsm connext ncbi_crypt bdb dbapi ctools gui gbench Tools / flags / paths: /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build/Makefile.mk Configuration header: /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/inc/ncbiconf_unix.h To build everything: cd /build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build && /usr/bin/make all_r or simply run /usr/bin/make in the current directory ******* CONFIGURATION SUCCESSFUL ******* make[1]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' cd c++/BUILD/build && \ make -j1 -f Makefile.flat all_projects="algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/" make[2]: Entering directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build' make[2]: Makefile.flat: No such file or directory make[2]: *** No rule to make target 'Makefile.flat'. Stop. make[2]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0/c++/BUILD/build' debian/rules:52: recipe for target 'override_dh_auto_build-arch' failed make[1]: *** [override_dh_auto_build-arch] Error 2 make[1]: Leaving directory '/build/ncbi-blast+-QriueX/ncbi-blast+-2.4.0' debian/rules:115: 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 2016-08-29T15:29:25Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /build/ncbi-blast+-QriueX Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 0 Build-Time: 47 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 24 Job: ncbi-blast+_2.4.0-3 Machine Architecture: amd64 Package: ncbi-blast+ Package-Time: 100 Source-Version: 2.4.0-3 Space: 0 Status: failed Version: 2.4.0-3 -------------------------------------------------------------------------------- Finished at 2016-08-29T15:29:25Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 100.440589954s DC-Time-Estimation: 100.440589954 versus expected 2301 (r/m: 21.909064961225504 ; m: 100.440589954)