DC-Build-Header: ncbi-blast+ 2.2.25-5 / Sun Sep 11 11:32:44 +0200 2011 Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-13.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ ncbi-blast+ 2.2.25-5 (amd64) 11 Sep 2011 11:56 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: ncbi-blast+ Version: 2.2.25-5 Source Version: 2.2.25-5 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (51.8 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'ncbi-blast+' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast+/trunk/ Need to get 11.9 MB of source archives. Get:1 http://localhost/debian/ sid/main ncbi-blast+ 2.2.25-5 (dsc) [2209 B] Get:2 http://localhost/debian/ sid/main ncbi-blast+ 2.2.25-5 (tar) [11.9 MB] Get:3 http://localhost/debian/ sid/main ncbi-blast+ 2.2.25-5 (diff) [16.4 kB] Fetched 11.9 MB in 0s (19.7 MB/s) Download complete and in download only mode Check arch ────────── 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+-qyfFeM/resolver-EKm0k5/apt_archive/sbuild-build-depends-core-dummy.deb'. OK 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 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64c-a8b3fef8-0c15-409a-b969-cdcc328a3bf1/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time dpkg-deb: building package `sbuild-build-depends-ncbi-blast+-dummy' in `/build/ncbi-blast+-qyfFeM/resolver-UikyYZ/apt_archive/sbuild-build-depends-ncbi-blast+-dummy.deb'. OK 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 extra packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libboost-test-dev libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libbz2-dev libcroco3 libglib2.0-0 libicu44 libmagic1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt time zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.46-doc libboost-date-time1.46-dev libboost-filesystem1.46-dev libboost-graph-parallel1.46-dev libboost-graph1.46-dev libboost-iostreams1.46-dev libboost-math1.46-dev libboost-mpi1.46-dev libboost-program-options1.46-dev libboost-python1.46-dev libboost-random1.46-dev libboost-regex1.46-dev libboost-serialization1.46-dev libboost-signals1.46-dev libboost-system1.46-dev libboost-thread1.46-dev libboost-wave1.46-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop www-browser libmail-box-perl procmail graphviz Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libboost-test-dev libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libbz2-dev libcroco3 libglib2.0-0 libicu44 libmagic1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-ncbi-blast+-dummy time zlib1g-dev 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 26.1 MB/26.1 MB of archives. After this operation, 131 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 libpcrecpp0 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 time autotools-dev html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper diffstat libicu44 libboost1.46-dev libboost-test1.46.1 libboost-test1.46-dev libboost-test-dev libbz2-dev libpcre3-dev quilt zlib1g-dev sbuild-build-depends-ncbi-blast+-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main libpcrecpp0 amd64 8.12-4 [113 kB] Get:4 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:5 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:6 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:7 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:8 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:9 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:10 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:11 http://localhost/debian/ sid/main time amd64 1.7-23.1 [33.1 kB] Get:12 http://localhost/debian/ sid/main autotools-dev all 20110511.1 [73.8 kB] Get:13 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:14 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:15 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:16 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:17 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:18 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:19 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:20 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:21 http://localhost/debian/ sid/main diffstat amd64 1.54-1 [29.0 kB] Get:22 http://localhost/debian/ sid/main libicu44 amd64 4.4.2-2 [7065 kB] Get:23 http://localhost/debian/ sid/main libboost1.46-dev amd64 1.46.1-7 [7832 kB] Get:24 http://localhost/debian/ sid/main libboost-test1.46.1 amd64 1.46.1-7 [259 kB] Get:25 http://localhost/debian/ sid/main libboost-test1.46-dev amd64 1.46.1-7 [646 kB] Get:26 http://localhost/debian/ sid/main libboost-test-dev amd64 1.46.1.1 [2530 B] Get:27 http://localhost/debian/ sid/main libbz2-dev amd64 1.0.5-7 [32.0 kB] Get:28 http://localhost/debian/ sid/main libpcre3-dev amd64 8.12-4 [307 kB] Get:29 http://localhost/debian/ sid/main quilt all 0.48-7 [354 kB] Get:30 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Extracting templates from packages: 96% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 26.1 MB in 0s (56.0 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package libpcrecpp0. Unpacking libpcrecpp0 (from .../libpcrecpp0_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. 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Unpacking sbuild-build-depends-ncbi-blast+-dummy (from .../sbuild-build-depends-ncbi-blast+-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up libpcre3 (8.12-4) ... Setting up libpcrecpp0 (8.12-4) ... Setting up bsdmainutils (8.2.3) ... 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 groff-base (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up time (1.7-23.1) ... Ignoring install-info called from maintainer script The package time should be rebuilt with new debhelper to get trigger support Setting up autotools-dev (20110511.1) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up diffstat (1.54-1) ... Setting up libicu44 (4.4.2-2) ... Setting up libboost1.46-dev (1.46.1-7) ... Setting up libboost-test1.46.1 (1.46.1-7) ... Setting up libboost-test1.46-dev (1.46.1-7) ... Setting up libboost-test-dev (1.46.1.1) ... Setting up libbz2-dev (1.0.5-7) ... Setting up libpcre3-dev (8.12-4) ... Setting up quilt (0.48-7) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ... Setting up sbuild-build-depends-ncbi-blast+-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-test-dev_1.46.1.1 libboost-test1.46-dev_1.46.1-7 libboost-test1.46.1_1.46.1-7 libboost1.46-dev_1.46.1-7 libbz2-1.0_1.0.5-7 libbz2-dev_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libicu44_4.4.2-2 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpcre3-dev_8.12-4 libpcrecpp0_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ncbi-blast+-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 time_1.7-23.1 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Mon Aug 29 19:19:29 2011 CEST using RSA key ID F14A64A2 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./ncbi-blast+_2.2.25-5.dsc dpkg-source: info: extracting ncbi-blast+ in ncbi-blast+-2.2.25 dpkg-source: info: unpacking ncbi-blast+_2.2.25.orig.tar.gz dpkg-source: info: unpacking ncbi-blast+_2.2.25-5.debian.tar.gz dpkg-source: info: applying hurd_fixes dpkg-source: info: applying legacy_rename_rpsblast dpkg-source: info: applying fix_checks dpkg-source: info: applying fix_gcc46_errors dpkg-source: info: applying support_other_cpus dpkg-source: info: applying fix_lib_deps dpkg-source: info: applying no_multiarch_rpath Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: source package ncbi-blast+ dpkg-buildpackage: source version 2.2.25-5 dpkg-source --before-build ncbi-blast+-2.2.25 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean -Dc++ --with autotools_dev --with quilt dh_testdir -O-Dc\+\+ dh_auto_clean -O-Dc\+\+ dh_autotools-dev_restoreconfig -O-Dc\+\+ dh_quilt_unpatch -O-Dc\+\+ Removing patch no_multiarch_rpath Restoring c++/src/build-system/configure.ac Restoring c++/src/build-system/configure Removing patch fix_lib_deps Restoring c++/src/serial/Makefile.serial.lib Restoring c++/src/corelib/Makefile.test_mt.lib Restoring c++/src/corelib/Makefile.test_boost.lib Restoring c++/src/util/xregexp/Makefile.xregexp.lib Restoring c++/src/util/Makefile.util.lib Restoring c++/src/util/sequtil/Makefile.sequtil.lib Restoring c++/src/util/compress/api/Makefile.compress.lib Restoring c++/src/objmgr/split/Makefile.id2_split.lib Restoring c++/src/objmgr/util/Makefile.util.lib Restoring c++/src/connect/ext/Makefile.xconnext.lib Restoring c++/src/connect/Makefile.xconnect.lib Restoring c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib Restoring c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib Restoring c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib Restoring c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib Restoring c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib Restoring c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib Restoring c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib Restoring c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib Restoring c++/src/objtools/blast/services/Makefile.blast_services.lib Restoring c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib Restoring c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib Restoring c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib Restoring c++/src/objtools/simple/Makefile.xobjsimple.lib Restoring c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib Restoring c++/src/objtools/readers/Makefile.xobjread.lib Restoring c++/src/objtools/alnmgr/Makefile.alnmgr.lib Restoring c++/src/objtools/align_format/Makefile.align_format.lib Restoring c++/src/objects/seqsplit/Makefile.seqsplit.lib Restoring c++/src/objects/seqset/Makefile.seqset.lib Restoring c++/src/objects/seqcode/Makefile.seqcode.lib Restoring c++/src/objects/seq/Makefile.seq.lib Restoring c++/src/objects/pub/Makefile.pub.lib Restoring c++/src/objects/medline/Makefile.medline.lib Restoring c++/src/objects/id2/Makefile.id2.lib Restoring c++/src/objects/id1/Makefile.id1.lib Restoring c++/src/objects/genomecoll/Makefile.genome_collection.lib Restoring c++/src/objects/general/Makefile.general.lib Restoring c++/src/objects/blastdb/Makefile.blastdb.lib Restoring c++/src/objects/biblio/Makefile.biblio.lib Restoring c++/src/objects/submit/Makefile.submit.lib Restoring c++/src/objects/seqedit/Makefile.seqedit.lib Restoring c++/src/objects/scoremat/Makefile.scoremat.lib Restoring c++/src/objects/entrez2/Makefile.entrez2cli.lib Restoring c++/src/objects/entrez2/Makefile.entrez2.lib Restoring c++/src/objects/blastxml/Makefile.blastxml.lib Restoring c++/src/objects/blast/Makefile.blast.lib Restoring c++/src/objects/blast/Makefile.xnetblastcli.lib Restoring c++/src/html/Makefile.html.lib Restoring c++/src/cgi/Makefile.cgi.lib Restoring c++/src/algo/segmask/Makefile.xalgosegmask.lib Restoring c++/src/algo/dustmask/Makefile.xalgodustmask.lib Restoring c++/src/algo/winmask/Makefile.xalgowinmask.lib Restoring c++/src/algo/blast/Makefile.blast_macros.mk Restoring c++/src/algo/blast/blastinput/Makefile.blastinput.lib Restoring c++/src/algo/blast/api/Makefile.xblast.lib Restoring c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib Restoring c++/src/algo/blast/format/Makefile.xblastformat.lib Restoring c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app Restoring c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib Restoring c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app Restoring c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib Restoring c++/src/algo/blast/core/Makefile.blast.lib Removing patch support_other_cpus Restoring c++/src/objects/seq/seq_id_tree.cpp Restoring c++/src/objects/seq/seq_id_handle.cpp Restoring c++/include/corelib/ncbiatomic.h Restoring c++/include/corelib/impl/ncbi_atomic_defs.h Removing patch fix_gcc46_errors Restoring c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp Restoring c++/include/corelib/ncbistre.hpp Removing patch fix_checks Restoring c++/src/build-system/Makefile.meta.in Restoring c++/scripts/common/check/check_add.sh Removing patch legacy_rename_rpsblast Restoring c++/src/app/blast/legacy_blast.pl Removing patch hurd_fixes Restoring c++/src/connect/ext/ncbi_localnet.c Restoring c++/src/connect/ncbi_socket_cxx.cpp Restoring c++/src/build-system/configure.ac Restoring c++/src/build-system/configure No patches applied debian/rules override_dh_clean make[1]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25' dh_clean for x in c++/src/objects/*/*.files; do \ (cd `dirname $x` && ../../../BUILD/build/new_module.sh \ `basename $x .files`.module purge_sources); \ done /bin/sh: 2: cd: can't cd to c++/src/objects/Makefile.in make[1]: [override_dh_clean] Error 2 (ignored) rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile rm -f c++/src/objects/blastxml/blastxml.module make[1]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25' dpkg-source -b ncbi-blast+-2.2.25 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override) dpkg-source: info: applying hurd_fixes dpkg-source: info: applying legacy_rename_rpsblast dpkg-source: info: applying fix_checks dpkg-source: info: applying fix_gcc46_errors dpkg-source: info: applying support_other_cpus dpkg-source: info: applying fix_lib_deps dpkg-source: info: applying no_multiarch_rpath dpkg-source: info: building ncbi-blast+ using existing ./ncbi-blast+_2.2.25.orig.tar.gz dpkg-source: info: building ncbi-blast+ in ncbi-blast+_2.2.25-5.debian.tar.gz dpkg-source: info: building ncbi-blast+ in ncbi-blast+_2.2.25-5.dsc debian/rules build dh build -Dc++ --with autotools_dev --with quilt dh_testdir -O-Dc\+\+ dh_autotools-dev_updateconfig -O-Dc\+\+ dh_quilt_patch -O-Dc\+\+ File series fully applied, ends at patch no_multiarch_rpath debian/rules override_dh_auto_configure make[1]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25' cd c++ && LD_LIBRARY_PATH=/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/lib${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 LDFLAGS='-Wl,--as-needed -Wl,--enable-new-dtags' --without-debug configure: loading site script ./src/build-system/config.site configure: creating cache config.cache checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-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 ANSI C... none needed 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 supports -Wl,-E... yes checking whether ln -s works... yes checking for ranlib... ranlib checking for ar... ar cr checking ranlib's effectiveness... neutral checking for ccache... no checking for tail... /usr/bin/tail checking whether /usr/bin/tail accepts modern syntax (-n N)... yes checking for egrep... grep -E checking how to run grep -E quietly... grep -E -q checking for valgrind... no checking how to run the C++ preprocessor... /usr/bin/g++ -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 for size_t... yes checking for size_t... (cached) yes checking size of size_t... 8 checking for amq... no checking whether /usr/bin/gcc supports -Wl,--no-allow-shlib-undefined... no checking how to run the C preprocessor... /usr/bin/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 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 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 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 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 netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking netinet/tcp.h usability... yes checking netinet/tcp.h presence... yes checking for netinet/tcp.h... yes checking paths.h usability... yes checking paths.h presence... yes checking for paths.h... yes checking signal.h usability... yes checking signal.h presence... yes checking for signal.h... yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes 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 euidaccess... yes checking for atoll... yes checking for basename... yes checking for lchown... yes checking for fseeko... yes checking for getpagesize... yes checking for getpass... yes checking for getpassphrase... no checking for getpwuid... yes checking for getrusage... yes checking for gettimeofday... yes checking for getuid... yes checking for readpassphrase... no checking for readv... yes checking for usleep... yes checking for asprintf... yes checking for vasprintf... yes checking for vsnprintf... yes checking for select... yes checking for statfs... yes checking for statvfs... yes checking for strcasecmp... yes checking for strlcat... no checking for strlcpy... no checking for strdup... yes checking for strndup... yes checking for strtok_r... yes checking for sysmp... no checking for timegm... yes checking for utimes... yes checking for lutimes... yes checking for writev... yes checking return type of signal handlers... void checking whether select updates the timeout when interrupted... yes checking whether strcasecmp treats letters as lowercase... yes checking for Linux-like sysinfo with 1 arg... yes checking for getloadavg... yes checking for readdir_r... 3 checking for an ANSI C-conforming const... yes checking whether byte ordering is bigendian... no checking whether char is unsigned... no checking for char... yes checking size of char... 1 checking for double... yes checking size of double... 8 checking for float... yes checking size of float... 4 checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 8 checking for long double... yes checking size of long double... 16 checking for long long... yes checking size of long long... 8 checking for short... yes checking size of short... 2 checking for void*... yes checking size of void*... 8 checking for __int64... no checking size of __int64... 0 checking for intptr_t... yes checking for uintptr_t... yes checking for struct sockaddr_in.sin_len... no checking for struct tm.tm_zone... yes checking 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 whether C++ streams delete their buffers... no checking for std::char_traits::... yes checking for std::is_sorted<> in ... no checking for SysV semaphores... yes checking for union semun... no checking which way the stack grows... down 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... __forceinline 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 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 in-house NCBI resources are available... no checking for gethostbyname in -lnsl... yes checking for connect in -lsocket... no checking for res_search in -lresolv... yes checking for inet_ntoa_r... no checking for getaddrinfo... yes checking for getnameinfo... yes checking for freehostent... no checking for gethostent_r... yes checking for getipnodebyaddr... no checking for getipnodebyname... no checking for inet_ntop... yes checking for erf... yes checking for library containing kstat_open... no checking for library containing rstat... no checking for library containing setkey... -lcrypt checking for library containing dlopen... -ldl checking for library containing uuid_generate... no checking for library containing fuse_loop... no checking for library containing clock_gettime... -lrt checking for library containing cplus_demangle... no checking for nanosleep... yes checking for 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 libgnutls-config... no checking for libgnutls... no checking for libssl... no checking for reentrant Sybase libraries... no checking for Sybase in ... no checking for FreeTDS in /netopt/Sybase/clients-mssql/current... no checking for mysql_config... no checking for Berkeley DB libraries in /BerkeleyDB... no checking for python... no checking for python2.3... no checking for python2.4... no checking for python2.5... no checking for CPPUNIT in /cppunit... no checking Boost version... 1_46_1 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... -mt (autodetected) checking for Boost.Regex in /boost... no checking for Boost.Spirit in /boost... yes checking for Boost.Test in /boost... included-only checking for Boost.Threads in /boost... no checking for the NCBI C toolkit in ... 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 FLTK in /fltk... no checking for wxWindows in /wxwin... no checking for wx-config... no checking for wxWidgets in /wxwidgets... no checking for FastCGI libraries in /fcgi-current... no checking for FCGX_Accept_r... no checking for NCBI SSS directories 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/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/serial/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/connect/ext/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/connect/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/objmgr/split/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/objmgr/util/unit_test/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/objmgr/util/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/objmgr/Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/./Makefile config.status: creating /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/inc/ncbiconf_unix.h config.status: executing default commands /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/build-system/Makefile.mk.in:577: duplicate definition of GENBANK_READER_PUBSEQOS_LDEP /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/build-system/Makefile.mk.in:576: original definition here /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib/ncbicfg.c is updated project_tree_builder is not found at /net/snowman/vol/export2/win-coremake/App/Ncbi/cppcore/ptb/Linux64/3.3.1/project_tree_builder Will build project_tree_builder locally ********************************************************************** Building project_tree_builder ********************************************************************** make[2]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[3]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[3]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[3]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `export-headers'. make[4]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `export-headers'. make[4]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `export-headers'. make[4]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' /usr/bin/g++ -c -Wall -Wno-format-y2k -pthread -O2 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/inc -I/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp -o blob_storage.o In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:2673:11: error: variable type 'CMask' is an abstract class CMask masks_empty; ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:48: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbi_mask.hpp:87:18: note: unimplemented pure virtual method 'Match' in 'CMask' virtual bool Match(const string& str, ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2654:9: error: use of undeclared identifier 'x_Assign' x_Assign(other); ^ this-> /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2726:5: note: in instantiation of member function 'ncbi::CParseTemplException::CParseTemplException' requested here NCBI_EXCEPTION_DEFAULT2(CStringException, ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1309:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:876:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2726:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT2(CStringException, ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1309:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2726:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT2(CStringException, ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2727:9: note: instantiated from: CParseTemplException, std::string::size_type); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:785:18: note: must qualify identifier to find this declaration in dependent base class virtual void x_Assign(const CException& src); ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:5: error: use of undeclared identifier 'x_Assign' NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:915:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:847:9: note: instantiated from: x_Assign(other); \ ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: in instantiation of member function 'ncbi::CErrnoTemplException::CErrnoTemplException' requested here NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:876:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:49: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:785:18: note: must qualify identifier to find this declaration in dependent base class virtual void x_Assign(const CException& src); ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1170:9: error: use of undeclared identifier 'x_Assign' x_Assign(other); ^ this-> /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:5: note: in instantiation of member function 'ncbi::CErrnoTemplExceptionEx::CErrnoTemplExceptionEx' requested here NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:915:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:84: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: in instantiation of member function 'ncbi::CErrnoTemplException::CErrnoTemplException' requested here NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:876:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:49: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:785:18: note: must qualify identifier to find this declaration in dependent base class virtual void x_Assign(const CException& src); ^ 4 errors generated. make[4]: *** [blob_storage.o] Error 1 make[4]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' rm -f libxncbi.so .xncbi.dep .libxncbi.so.stamp if [ '/bin/bash /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/scripts/common/impl/if_diff.sh "ln -f"' != '@:' -a -d /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/status -a -w /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/status -a /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/src/corelib != . ]; then \ rm -f /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so \ /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/status/.xncbi.dep /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/status/.xncbi.dep; \ [ '@# ' = '@# ' ] || \ rm -f /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so; \ fi make[4]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' FAILED: src/corelib/Makefile.corelib.lib make[3]: *** [all.nonusr] Error 2 make[3]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[2]: *** [all.needs-reqs] Error 2 make[2]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' ------------------------------------------------------ Current dir: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/corelib [create_flat_makefile.sh] FAILED (status 2): make =============================================================================== NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running For the available configuration flags run: ./configure --help CFLAGS = -Wall -Wno-format-y2k -pthread -O2 -fPIC CXXFLAGS = -Wall -Wno-format-y2k -pthread -O2 -fPIC CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE LDFLAGS = -pthread -Wl,--as-needed -Wl,--enable-new-dtags -O LIBRARIES: build as dynamic by default FEATURES: GCC MT DLL DLL_BUILD unix WinMain Linux PACKAGES: enabled: Z BZ2 PCRE Boost.Spirit Boost.Test.Included disabled: UUID FUSE LocalZ LocalBZ2 LZO LocalPCRE GNUTLS OPENSSL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON PYTHON23 PYTHON24 PYTHON25 CPPUNIT Boost.Regex Boost.Test Boost.Threads C-Toolkit OpenGL MESA GLUT GLEW FLTK wxWindows wxWidgets wx2.8 Fast-CGI LocalNCBILS LocalSSS LocalMSGMAIL2 SSSUTILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXML LIBXSLT Xerces Xalan SQLITE SQLITE3 SQLITE3ASYNC OECHEM SGE MUPARSER HDF5 JPEG PNG TIFF UNGIF GIF XPM FreeType PROJECTS: enabled: cgi local_lbsm connext ncbi_crypt serial objects app algo disabled: bdb dbapi ctools gui gbench Tools / flags / paths: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build/Makefile.mk Configuration header: /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/inc/ncbiconf_unix.h To build everything: cd /build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build && make all_r or simply run make in the current directory ******* CONFIGURATION SUCCESSFUL ******* make[1]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25' debian/rules override_dh_auto_build make[1]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25' cd c++/BUILD/build && make -f Makefile.flat all_projects="algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/" make[2]: Makefile.flat: No such file or directorymake[2]: Entering directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build' make[2]: *** No rule to make target `Makefile.flat'. Stop. make[2]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25/c++/BUILD/build' make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/build/ncbi-blast+-qyfFeM/ncbi-blast+-2.2.25' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1157 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-a8b3fef8-0c15-409a-b969-cdcc328a3bf1/build/ncbi-blast+-qyfFeM Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 79892 Build-Time: 39 Distribution: lsid64c Fail-Stage: build Install-Time: 7 Job: ncbi-blast+_2.2.25-5 Package: ncbi-blast+ Package-Time: 60 Source-Version: 2.2.25-5 Space: 79892 Status: attempted Version: 2.2.25-5 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1157 Build needed 00:01:00, 79892k disc space DC-Message: Failed, but took only 1472.603422. Retrying, you never know. Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-13.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ ncbi-blast+ 2.2.25-5 (amd64) 11 Sep 2011 12:13 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: ncbi-blast+ Version: 2.2.25-5 Source Version: 2.2.25-5 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (63.1 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'ncbi-blast+' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast+/trunk/ Need to get 11.9 MB of source archives. Get:1 http://localhost/debian/ sid/main ncbi-blast+ 2.2.25-5 (dsc) [2209 B] Get:2 http://localhost/debian/ sid/main ncbi-blast+ 2.2.25-5 (tar) [11.9 MB] Get:3 http://localhost/debian/ sid/main ncbi-blast+ 2.2.25-5 (diff) [16.4 kB] Fetched 11.9 MB in 0s (61.3 MB/s) Download complete and in download only mode Check arch ────────── 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+-VkI4lI/resolver-BIZ915/apt_archive/sbuild-build-depends-core-dummy.deb'. OK 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 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64c-228f4f32-72fe-47cc-95f9-80ac6e3c49b6/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time dpkg-deb: building package `sbuild-build-depends-ncbi-blast+-dummy' in `/build/ncbi-blast+-VkI4lI/resolver-jNsbjB/apt_archive/sbuild-build-depends-ncbi-blast+-dummy.deb'. OK 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 extra packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libboost-test-dev libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libbz2-dev libcroco3 libglib2.0-0 libicu44 libmagic1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt time zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.46-doc libboost-date-time1.46-dev libboost-filesystem1.46-dev libboost-graph-parallel1.46-dev libboost-graph1.46-dev libboost-iostreams1.46-dev libboost-math1.46-dev libboost-mpi1.46-dev libboost-program-options1.46-dev libboost-python1.46-dev libboost-random1.46-dev libboost-regex1.46-dev libboost-serialization1.46-dev libboost-signals1.46-dev libboost-system1.46-dev libboost-thread1.46-dev libboost-wave1.46-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop www-browser libmail-box-perl procmail graphviz Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libboost-test-dev libboost-test1.46-dev libboost-test1.46.1 libboost1.46-dev libbz2-dev libcroco3 libglib2.0-0 libicu44 libmagic1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-ncbi-blast+-dummy time zlib1g-dev 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 26.1 MB/26.1 MB of archives. After this operation, 131 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 libpcrecpp0 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 time autotools-dev html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper diffstat libicu44 libboost1.46-dev libboost-test1.46.1 libboost-test1.46-dev libboost-test-dev libbz2-dev libpcre3-dev quilt zlib1g-dev sbuild-build-depends-ncbi-blast+-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main libpcrecpp0 amd64 8.12-4 [113 kB] Get:4 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:5 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:6 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:7 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:8 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:9 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:10 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:11 http://localhost/debian/ sid/main time amd64 1.7-23.1 [33.1 kB] Get:12 http://localhost/debian/ sid/main autotools-dev all 20110511.1 [73.8 kB] Get:13 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:14 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:15 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:16 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:17 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:18 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:19 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:20 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:21 http://localhost/debian/ sid/main diffstat amd64 1.54-1 [29.0 kB] Get:22 http://localhost/debian/ sid/main libicu44 amd64 4.4.2-2 [7065 kB] Get:23 http://localhost/debian/ sid/main libboost1.46-dev amd64 1.46.1-7 [7832 kB] Get:24 http://localhost/debian/ sid/main libboost-test1.46.1 amd64 1.46.1-7 [259 kB] Get:25 http://localhost/debian/ sid/main libboost-test1.46-dev amd64 1.46.1-7 [646 kB] Get:26 http://localhost/debian/ sid/main libboost-test-dev amd64 1.46.1.1 [2530 B] Get:27 http://localhost/debian/ sid/main libbz2-dev amd64 1.0.5-7 [32.0 kB] Get:28 http://localhost/debian/ sid/main libpcre3-dev amd64 8.12-4 [307 kB] Get:29 http://localhost/debian/ sid/main quilt all 0.48-7 [354 kB] Get:30 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Extracting templates from packages: 96% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 26.1 MB in 0s (60.7 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package libpcrecpp0. Unpacking libpcrecpp0 (from .../libpcrecpp0_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. 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Unpacking sbuild-build-depends-ncbi-blast+-dummy (from .../sbuild-build-depends-ncbi-blast+-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up libpcre3 (8.12-4) ... Setting up libpcrecpp0 (8.12-4) ... Setting up bsdmainutils (8.2.3) ... 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 groff-base (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up time (1.7-23.1) ... Ignoring install-info called from maintainer script The package time should be rebuilt with new debhelper to get trigger support Setting up autotools-dev (20110511.1) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up diffstat (1.54-1) ... Setting up libicu44 (4.4.2-2) ... Setting up libboost1.46-dev (1.46.1-7) ... Setting up libboost-test1.46.1 (1.46.1-7) ... Setting up libboost-test1.46-dev (1.46.1-7) ... Setting up libboost-test-dev (1.46.1.1) ... Setting up libbz2-dev (1.0.5-7) ... Setting up libpcre3-dev (8.12-4) ... Setting up quilt (0.48-7) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ... Setting up sbuild-build-depends-ncbi-blast+-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-test-dev_1.46.1.1 libboost-test1.46-dev_1.46.1-7 libboost-test1.46.1_1.46.1-7 libboost1.46-dev_1.46.1-7 libbz2-1.0_1.0.5-7 libbz2-dev_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libicu44_4.4.2-2 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpcre3-dev_8.12-4 libpcrecpp0_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ncbi-blast+-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 time_1.7-23.1 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Mon Aug 29 19:19:29 2011 CEST using RSA key ID F14A64A2 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./ncbi-blast+_2.2.25-5.dsc dpkg-source: info: extracting ncbi-blast+ in ncbi-blast+-2.2.25 dpkg-source: info: unpacking ncbi-blast+_2.2.25.orig.tar.gz dpkg-source: info: unpacking ncbi-blast+_2.2.25-5.debian.tar.gz dpkg-source: info: applying hurd_fixes dpkg-source: info: applying legacy_rename_rpsblast dpkg-source: info: applying fix_checks dpkg-source: info: applying fix_gcc46_errors dpkg-source: info: applying support_other_cpus dpkg-source: info: applying fix_lib_deps dpkg-source: info: applying no_multiarch_rpath Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: source package ncbi-blast+ dpkg-buildpackage: source version 2.2.25-5 dpkg-source --before-build ncbi-blast+-2.2.25 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean -Dc++ --with autotools_dev --with quilt dh_testdir -O-Dc\+\+ dh_auto_clean -O-Dc\+\+ dh_autotools-dev_restoreconfig -O-Dc\+\+ dh_quilt_unpatch -O-Dc\+\+ Removing patch no_multiarch_rpath Restoring c++/src/build-system/configure.ac Restoring c++/src/build-system/configure Removing patch fix_lib_deps Restoring c++/src/serial/Makefile.serial.lib Restoring c++/src/corelib/Makefile.test_mt.lib Restoring c++/src/corelib/Makefile.test_boost.lib Restoring c++/src/util/xregexp/Makefile.xregexp.lib Restoring c++/src/util/Makefile.util.lib Restoring c++/src/util/sequtil/Makefile.sequtil.lib Restoring c++/src/util/compress/api/Makefile.compress.lib Restoring c++/src/objmgr/split/Makefile.id2_split.lib Restoring c++/src/objmgr/util/Makefile.util.lib Restoring c++/src/connect/ext/Makefile.xconnext.lib Restoring c++/src/connect/Makefile.xconnect.lib Restoring c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib Restoring c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib Restoring c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib Restoring c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib Restoring c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib Restoring c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib Restoring c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib Restoring c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib Restoring c++/src/objtools/blast/services/Makefile.blast_services.lib Restoring c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib Restoring c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib Restoring c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib Restoring c++/src/objtools/simple/Makefile.xobjsimple.lib Restoring c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib Restoring c++/src/objtools/readers/Makefile.xobjread.lib Restoring c++/src/objtools/alnmgr/Makefile.alnmgr.lib Restoring c++/src/objtools/align_format/Makefile.align_format.lib Restoring c++/src/objects/seqsplit/Makefile.seqsplit.lib Restoring c++/src/objects/seqset/Makefile.seqset.lib Restoring c++/src/objects/seqcode/Makefile.seqcode.lib Restoring c++/src/objects/seq/Makefile.seq.lib Restoring c++/src/objects/pub/Makefile.pub.lib Restoring c++/src/objects/medline/Makefile.medline.lib Restoring c++/src/objects/id2/Makefile.id2.lib Restoring c++/src/objects/id1/Makefile.id1.lib Restoring c++/src/objects/genomecoll/Makefile.genome_collection.lib Restoring c++/src/objects/general/Makefile.general.lib Restoring c++/src/objects/blastdb/Makefile.blastdb.lib Restoring c++/src/objects/biblio/Makefile.biblio.lib Restoring c++/src/objects/submit/Makefile.submit.lib Restoring c++/src/objects/seqedit/Makefile.seqedit.lib Restoring c++/src/objects/scoremat/Makefile.scoremat.lib Restoring c++/src/objects/entrez2/Makefile.entrez2cli.lib Restoring c++/src/objects/entrez2/Makefile.entrez2.lib Restoring c++/src/objects/blastxml/Makefile.blastxml.lib Restoring c++/src/objects/blast/Makefile.blast.lib Restoring c++/src/objects/blast/Makefile.xnetblastcli.lib Restoring c++/src/html/Makefile.html.lib Restoring c++/src/cgi/Makefile.cgi.lib Restoring c++/src/algo/segmask/Makefile.xalgosegmask.lib Restoring c++/src/algo/dustmask/Makefile.xalgodustmask.lib Restoring c++/src/algo/winmask/Makefile.xalgowinmask.lib Restoring c++/src/algo/blast/Makefile.blast_macros.mk Restoring c++/src/algo/blast/blastinput/Makefile.blastinput.lib Restoring c++/src/algo/blast/api/Makefile.xblast.lib Restoring c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib Restoring c++/src/algo/blast/format/Makefile.xblastformat.lib Restoring c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app Restoring c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib Restoring c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app Restoring c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib Restoring c++/src/algo/blast/core/Makefile.blast.lib Removing patch support_other_cpus Restoring c++/src/objects/seq/seq_id_tree.cpp Restoring c++/src/objects/seq/seq_id_handle.cpp Restoring c++/include/corelib/ncbiatomic.h Restoring c++/include/corelib/impl/ncbi_atomic_defs.h Removing patch fix_gcc46_errors Restoring c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp Restoring c++/include/corelib/ncbistre.hpp Removing patch fix_checks Restoring c++/src/build-system/Makefile.meta.in Restoring c++/scripts/common/check/check_add.sh Removing patch legacy_rename_rpsblast Restoring c++/src/app/blast/legacy_blast.pl Removing patch hurd_fixes Restoring c++/src/connect/ext/ncbi_localnet.c Restoring c++/src/connect/ncbi_socket_cxx.cpp Restoring c++/src/build-system/configure.ac Restoring c++/src/build-system/configure No patches applied debian/rules override_dh_clean make[1]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25' dh_clean for x in c++/src/objects/*/*.files; do \ (cd `dirname $x` && ../../../BUILD/build/new_module.sh \ `basename $x .files`.module purge_sources); \ done /bin/sh: 2: cd: can't cd to c++/src/objects/Makefile.in make[1]: [override_dh_clean] Error 2 (ignored) rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile rm -f c++/src/objects/blastxml/blastxml.module make[1]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25' dpkg-source -b ncbi-blast+-2.2.25 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override) dpkg-source: info: applying hurd_fixes dpkg-source: info: applying legacy_rename_rpsblast dpkg-source: info: applying fix_checks dpkg-source: info: applying fix_gcc46_errors dpkg-source: info: applying support_other_cpus dpkg-source: info: applying fix_lib_deps dpkg-source: info: applying no_multiarch_rpath dpkg-source: info: building ncbi-blast+ using existing ./ncbi-blast+_2.2.25.orig.tar.gz dpkg-source: info: building ncbi-blast+ in ncbi-blast+_2.2.25-5.debian.tar.gz dpkg-source: info: building ncbi-blast+ in ncbi-blast+_2.2.25-5.dsc debian/rules build dh build -Dc++ --with autotools_dev --with quilt dh_testdir -O-Dc\+\+ dh_autotools-dev_updateconfig -O-Dc\+\+ dh_quilt_patch -O-Dc\+\+ File series fully applied, ends at patch no_multiarch_rpath debian/rules override_dh_auto_configure make[1]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25' cd c++ && LD_LIBRARY_PATH=/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/lib${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 LDFLAGS='-Wl,--as-needed -Wl,--enable-new-dtags' --without-debug configure: loading site script ./src/build-system/config.site configure: creating cache config.cache checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-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 ANSI C... none needed 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 supports -Wl,-E... yes checking whether ln -s works... yes checking for ranlib... ranlib 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checking for struct sockaddr_in.sin_len... no checking for struct tm.tm_zone... yes checking 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 whether C++ streams delete their buffers... no checking for std::char_traits::... yes checking for std::is_sorted<> in ... no checking for SysV semaphores... yes checking for union semun... no checking which way the stack grows... down 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... __forceinline 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 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 in-house NCBI resources are available... no checking for gethostbyname in -lnsl... yes checking for connect in -lsocket... no checking for res_search in -lresolv... yes checking for inet_ntoa_r... no checking for getaddrinfo... yes checking for getnameinfo... yes checking for freehostent... no checking for gethostent_r... yes checking for getipnodebyaddr... no checking for getipnodebyname... no checking for inet_ntop... yes checking for erf... yes checking for library containing kstat_open... no checking for library containing rstat... no checking for library containing setkey... -lcrypt checking for library containing dlopen... -ldl checking for library containing uuid_generate... no checking for library containing fuse_loop... no checking for library containing clock_gettime... -lrt checking for library containing cplus_demangle... no checking for nanosleep... yes checking for 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 libgnutls-config... no checking for libgnutls... no checking for libssl... no checking for reentrant Sybase libraries... no checking for Sybase in ... no checking for FreeTDS in /netopt/Sybase/clients-mssql/current... no checking for mysql_config... no checking for Berkeley DB libraries in /BerkeleyDB... no checking for python... no checking for python2.3... no checking for python2.4... no checking for python2.5... no checking for CPPUNIT in /cppunit... no checking Boost version... 1_46_1 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... -mt (autodetected) checking for Boost.Regex in /boost... no checking for Boost.Spirit in /boost... yes checking for Boost.Test in /boost... included-only checking for Boost.Threads in /boost... no checking for the NCBI C toolkit in ... 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 FLTK in /fltk... no checking for wxWindows in /wxwin... no checking for wx-config... no checking for wxWidgets in /wxwidgets... no checking for FastCGI libraries in /fcgi-current... no checking for FCGX_Accept_r... no checking for NCBI SSS directories in /sss/BUILD... no checking for SP directories in /SP... no checking for ORBacus in /corba/OB-4.0.1... no checking for ICU in /icu... no checking for libexpat... no checking for libsablot... no checking for libxml2... no checking for libxslt... no checking for xsltproc... : checking for Xerces-C++... no checking for Xalan-C++... no checking for libsqlite... no checking for libsqlite3... no checking for liboechem... no checking for libdrmaa... no checking for libmuparser... no checking for libhdf5_cpp... no checking for libjpeg... no checking for libpng... no checking for libtiff... no checking for libungif... no checking for libgif... no checking for libXpm in .... no checking for freetype-config... no configure: looking for configurables below /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++... configure: ...done updating cache config.cache configure: creating /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/status/config.status config.status: creating 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config.status: executing default commands /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/build-system/Makefile.mk.in:577: duplicate definition of GENBANK_READER_PUBSEQOS_LDEP /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/build-system/Makefile.mk.in:576: original definition here /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib/ncbicfg.c is updated project_tree_builder is not found at /net/snowman/vol/export2/win-coremake/App/Ncbi/cppcore/ptb/Linux64/3.3.1/project_tree_builder Will build project_tree_builder locally ********************************************************************** Building project_tree_builder ********************************************************************** make[2]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[3]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[3]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[3]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `export-headers'. make[4]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `export-headers'. make[4]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Nothing to be done for `export-headers'. make[4]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' /usr/bin/g++ -c -Wall -Wno-format-y2k -pthread -O2 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/inc -I/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp -o blob_storage.o In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:2673:11: error: variable type 'CMask' is an abstract class CMask masks_empty; ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:48: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbi_mask.hpp:87:18: note: unimplemented pure virtual method 'Match' in 'CMask' virtual bool Match(const string& str, ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2654:9: error: use of undeclared identifier 'x_Assign' x_Assign(other); ^ this-> /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2726:5: note: in instantiation of member function 'ncbi::CParseTemplException::CParseTemplException' requested here NCBI_EXCEPTION_DEFAULT2(CStringException, ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1309:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:876:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2726:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT2(CStringException, ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1309:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2726:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT2(CStringException, ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:2727:9: note: instantiated from: CParseTemplException, std::string::size_type); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:785:18: note: must qualify identifier to find this declaration in dependent base class virtual void x_Assign(const CException& src); ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:5: error: use of undeclared identifier 'x_Assign' NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:915:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:847:9: note: instantiated from: x_Assign(other); \ ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: in instantiation of member function 'ncbi::CErrnoTemplException::CErrnoTemplException' requested here NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:876:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:49: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:785:18: note: must qualify identifier to find this declaration in dependent base class virtual void x_Assign(const CException& src); ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1170:9: error: use of undeclared identifier 'x_Assign' x_Assign(other); ^ this-> /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:5: note: in instantiation of member function 'ncbi::CErrnoTemplExceptionEx::CErrnoTemplExceptionEx' requested here NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:915:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:1240:84: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException, CParent) ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: in instantiation of member function 'ncbi::CErrnoTemplException::CErrnoTemplException' requested here NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:876:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \ ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:894:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION(exception_class, base_class) ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:39: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/plugin_manager.hpp:72: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbidll.hpp:40: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:5: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbifile.hpp:172:49: note: instantiated from: NCBI_EXCEPTION_DEFAULT(CFileErrnoException, CFileErrnoException_Base); ^ In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib/blob_storage.cpp:33: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/blob_storage.hpp:36: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistd.hpp:37: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbistr.hpp:38: In file included from /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/tempstr.hpp:39: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/include/corelib/ncbiexpt.hpp:785:18: note: must qualify identifier to find this declaration in dependent base class virtual void x_Assign(const CException& src); ^ 4 errors generated. make[4]: *** [blob_storage.o] Error 1 make[4]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[4]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' rm -f libxncbi.so .xncbi.dep .libxncbi.so.stamp if [ '/bin/bash /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/scripts/common/impl/if_diff.sh "ln -f"' != '@:' -a -d /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/status -a -w /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/status -a /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/src/corelib != . ]; then \ rm -f /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so \ /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/status/.xncbi.dep /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/status/.xncbi.dep; \ [ '@# ' = '@# ' ] || \ rm -f /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/lib/libxncbi.so; \ fi make[4]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' FAILED: src/corelib/Makefile.corelib.lib make[3]: *** [all.nonusr] Error 2 make[3]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' make[2]: *** [all.needs-reqs] Error 2 make[2]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib' ------------------------------------------------------ Current dir: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/corelib [create_flat_makefile.sh] FAILED (status 2): make =============================================================================== NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running For the available configuration flags run: ./configure --help CFLAGS = -Wall -Wno-format-y2k -pthread -O2 -fPIC CXXFLAGS = -Wall -Wno-format-y2k -pthread -O2 -fPIC CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE LDFLAGS = -pthread -Wl,--as-needed -Wl,--enable-new-dtags -O LIBRARIES: build as dynamic by default FEATURES: GCC MT DLL DLL_BUILD unix WinMain Linux PACKAGES: enabled: Z BZ2 PCRE Boost.Spirit Boost.Test.Included disabled: UUID FUSE LocalZ LocalBZ2 LZO LocalPCRE GNUTLS OPENSSL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON PYTHON23 PYTHON24 PYTHON25 CPPUNIT Boost.Regex Boost.Test Boost.Threads C-Toolkit OpenGL MESA GLUT GLEW FLTK wxWindows wxWidgets wx2.8 Fast-CGI LocalNCBILS LocalSSS LocalMSGMAIL2 SSSUTILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXML LIBXSLT Xerces Xalan SQLITE SQLITE3 SQLITE3ASYNC OECHEM SGE MUPARSER HDF5 JPEG PNG TIFF UNGIF GIF XPM FreeType PROJECTS: enabled: cgi local_lbsm connext ncbi_crypt serial objects app algo disabled: bdb dbapi ctools gui gbench Tools / flags / paths: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build/Makefile.mk Configuration header: /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/inc/ncbiconf_unix.h To build everything: cd /build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build && make all_r or simply run make in the current directory ******* CONFIGURATION SUCCESSFUL ******* make[1]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25' debian/rules override_dh_auto_build make[1]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25' cd c++/BUILD/build && make -f Makefile.flat all_projects="algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/" make[2]: Makefile.flat: No such file or directory make[2]: Entering directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build' make[2]: *** No rule to make target `Makefile.flat'. Stop. make[2]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25/c++/BUILD/build' make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/build/ncbi-blast+-VkI4lI/ncbi-blast+-2.2.25' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1214 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-228f4f32-72fe-47cc-95f9-80ac6e3c49b6/build/ncbi-blast+-VkI4lI Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 79892 Build-Time: 42 Distribution: lsid64c Fail-Stage: build Install-Time: 6 Job: ncbi-blast+_2.2.25-5 Package: ncbi-blast+ Package-Time: 59 Source-Version: 2.2.25-5 Space: 79892 Status: attempted Version: 2.2.25-5 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1214 Build needed 00:00:59, 79892k disc space DC-Build-Status: Failed 2523.854473s ### Content of /var/log/daemon.log ### Sep 11 10:47:55 talc-13 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:06 talc-13 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:45 talc-13 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:48:49 talc-13 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:00 talc-13 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:11 talc-13 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:12 talc-13 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:25 talc-13 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:28 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:48 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:50 talc-13 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:59 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:10 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:25 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:32 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Sep 11 10:50:51 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Sep 11 10:51:06 talc-13 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long Sep 11 10:51:25 talc-13 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 2523.854473 versus expected 32000 (r/m: 11.6790194689644 ; m: 2523.854473)