DC-Build-Header: last-align 189-1 / Fri Jan 13 01:07:01 +0100 2012 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 stremi-39.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ last-align 189-1 (amd64) 13 Jan 2012 01:08 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: last-align Version: 189-1 Source Version: 189-1 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 3s (5423 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'last-align' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/last-align/trunk/ Need to get 238 kB of source archives. Get:1 http://localhost/debian/ sid/main last-align 189-1 (dsc) [2040 B] Get:2 http://localhost/debian/ sid/main last-align 189-1 (tar) [228 kB] Get:3 http://localhost/debian/ sid/main last-align 189-1 (diff) [7647 B] Fetched 238 kB in 0s (495 kB/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/last-align-jgfyzN/resolver-8bYdcr/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 10 not upgraded. Need to get 0 B/704 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 unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 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/lsid64b-52d6de43-372b-4d01-9270-7e00485fee42/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 (>= 8), cdbs, help2man (>= 1.36.4+nmu1), python-imaging 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 (>= 8), cdbs, help2man (>= 1.36.4+nmu1), python-imaging dpkg-deb: building package `sbuild-build-depends-last-align-dummy' in `/build/last-align-jgfyzN/resolver-3jOlak/apt_archive/sbuild-build-depends-last-align-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install last-align build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libdb4.8 libexpat1 libfreetype6 libglib2.0-0 libjpeg8 liblcms1 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-imaging python-minimal python2.6 python2.6-minimal python2.7 python2.7-minimal Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc groff liblcms-utils www-browser libmail-box-perl python-doc python-tk python-imaging-doc python-imaging-dbg python2.6-doc binfmt-support python2.7-doc Recommended packages: autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libdb4.8 libexpat1 libfreetype6 libglib2.0-0 libjpeg8 liblcms1 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-imaging python-minimal python2.6 python2.6-minimal python2.7 python2.7-minimal sbuild-build-depends-last-align-dummy 0 upgraded, 36 newly installed, 0 to remove and 10 not upgraded. Need to get 22.0 MB/22.0 MB of archives. After this operation, 66.0 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libssl1.0.0 liblocale-gettext-perl libpcre3 libglib2.0-0 libxml2 libcroco3 libexpat1 libfreetype6 libunistring0 libdb4.8 bsdmainutils groff-base man-db libmagic1 file gettext-base libsqlite3-0 mime-support python2.7-minimal python2.7 python-minimal python python2.6-minimal python2.6 cdbs html2text gettext intltool-debian po-debconf debhelper help2man libjpeg8 liblcms1 python-imaging sbuild-build-depends-last-align-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-3 [1143 kB] Get:3 http://localhost/debian/ sid/main liblocale-gettext-perl amd64 1.05-7+b1 [20.4 kB] Get:4 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:5 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:6 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:7 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:8 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7.2 [139 kB] Get:9 http://localhost/debian/ sid/main libfreetype6 amd64 2.4.8-1 [442 kB] Get:10 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:11 http://localhost/debian/ sid/main libdb4.8 amd64 4.8.30-11 [694 kB] Get:12 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:13 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:14 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:15 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:16 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:17 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:18 http://localhost/debian/ sid/main libsqlite3-0 amd64 3.7.9-3 [431 kB] Get:19 http://localhost/debian/ sid/main mime-support all 3.51-1 [35.0 kB] Get:20 http://localhost/debian/ sid/main python2.7-minimal amd64 2.7.2-10 [1766 kB] Get:21 http://localhost/debian/ sid/main python2.7 amd64 2.7.2-10 [2712 kB] Get:22 http://localhost/debian/ sid/main python-minimal all 2.7.2-9 [39.8 kB] Get:23 http://localhost/debian/ sid/main python all 2.7.2-9 [176 kB] Get:24 http://localhost/debian/ sid/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:25 http://localhost/debian/ sid/main python2.6 amd64 2.6.7-4 [2483 kB] Get:26 http://localhost/debian/ sid/main cdbs all 0.4.100 [77.1 kB] Get:27 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:28 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:29 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:30 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:31 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:32 http://localhost/debian/ sid/main help2man amd64 1.40.5 [95.6 kB] Get:33 http://localhost/debian/ sid/main libjpeg8 amd64 8c-2 [132 kB] Get:34 http://localhost/debian/ sid/main liblcms1 amd64 1.19.dfsg-1+b1 [112 kB] Get:35 http://localhost/debian/ sid/main python-imaging amd64 1.1.7-4 [457 kB] Extracting templates from packages: 83% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 22.0 MB in 0s (39.2 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_amd64.deb) ... Selecting previously unselected package liblocale-gettext-perl. Unpacking liblocale-gettext-perl (from .../liblocale-gettext-perl_1.05-7+b1_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... 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Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package libsqlite3-0. Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-3_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.2-10_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.2-9_all.deb) ... Selecting previously unselected package python2.6-minimal. 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Unpacking help2man (from .../help2man_1.40.5_amd64.deb) ... Selecting previously unselected package libjpeg8. Unpacking libjpeg8 (from .../libjpeg8_8c-2_amd64.deb) ... Selecting previously unselected package liblcms1. Unpacking liblcms1 (from .../liblcms1_1.19.dfsg-1+b1_amd64.deb) ... Selecting previously unselected package python-imaging. Unpacking python-imaging (from .../python-imaging_1.1.7-4_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-last-align-dummy. Unpacking sbuild-build-depends-last-align-dummy (from .../sbuild-build-depends-last-align-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libssl1.0.0 (1.0.0e-3) ... Setting up liblocale-gettext-perl (1.05-7+b1) ... Setting up libpcre3 (8.12-4) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libexpat1 (2.0.1-7.2) ... Setting up libfreetype6 (2.4.8-1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libdb4.8 (4.8.30-11) ... 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 (2.6.0.2-3) ... Building database of manual pages ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up libsqlite3-0 (3.7.9-3) ... Setting up mime-support (3.51-1) ... Setting up python2.7-minimal (2.7.2-10) ... Setting up python2.7 (2.7.2-10) ... Setting up python-minimal (2.7.2-9) ... Setting up python (2.7.2-9) ... Setting up python2.6-minimal (2.6.7-4) ... Setting up python2.6 (2.6.7-4) ... Setting up cdbs (0.4.100) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up help2man (1.40.5) ... Setting up libjpeg8 (8c-2) ... Setting up liblcms1 (1.19.dfsg-1+b1) ... Setting up python-imaging (1.1.7-4) ... Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 clang_3.0-5 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 help2man_1.40.5 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libfreetype6_2.4.8-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 libjpeg8_8c-2 liblcms1_1.19.dfsg-1+b1 libllvm3.0_3.0-5 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-3 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-imaging_1.1.7-4 python-minimal_2.7.2-9 python2.6_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_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 Sat Oct 22 11:39:21 2011 CEST using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./last-align_189-1.dsc dpkg-source: info: extracting last-align in last-align-189 dpkg-source: info: unpacking last-align_189.orig.tar.xz dpkg-source: info: unpacking last-align_189-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package last-align dpkg-buildpackage: source version 189-1 dpkg-source --before-build last-align-189 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean make[1]: *** No rule to make target `clean'. make[1]: Entering directory `/build/last-align-jgfyzN/last-align-189' make[1]: Leaving directory `/build/last-align-jgfyzN/last-align-189' make: [makefile-clean] Error 2 (ignored) dh_clean rm -f src/lastdb src/lastal src/lastex src/*.o dpkg-source -b last-align-189 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building last-align using existing ./last-align_189.orig.tar.xz dpkg-source: info: building last-align in last-align_189-1.debian.tar.gz dpkg-source: info: building last-align in last-align_189-1.dsc debian/rules build test -x debian/rules mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" --directory src make[1]: Entering directory `/build/last-align-jgfyzN/last-align-189/src' g++ -Wall -W -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -o lastdb Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc SubsetSuffixArraySort.cc MultiSequenceQual.cc lastdb.cc clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' MultiSequenceQual.cc:191:48: warning: array subscript is of type 'char' [-Wchar-subscripts] unsigned delimiterColumn = lettersToNumbers[' ']; ^~~~ 1 warning generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c CA_code/lambda_calculator.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from CA_code/lambda_calculator.c:12: CA_code/nrutil.c:207:37: warning: incompatible pointer types passing 'int **' to parameter of type 'double **' [-Wincompatible-pointer-types] for(i=n1h;i>=n1l;i--) free_dmatrix(m[i],n2l,n2h,n3l,n3h); ^~~~ 1 warning generated. g++ -Wall -W -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -o lastal Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastalArguments.cc io.cc fileMap.cc ScoreMatrix.cc DiagonalTable.cc SegmentPair.cc Alignment.cc XdropAligner.cc SegmentPairPot.cc AlignmentPot.cc GeneralizedAffineGapCosts.cc Centroid.cc LambdaCalculator.cc TwoQualityScoreMatrix.cc OneQualityScoreMatrix.cc QualityPssmMaker.cc GeneticCode.cc Xdrop3FrameAligner.cc gaplessXdrop.cc gaplessPssmXdrop.cc gaplessTwoQualityXdrop.cc AlignmentWrite.cc MultiSequenceQual.cc XdropAlignerPssm.cc lastal.cc lambda_calculator.o clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' ScoreMatrix.cc:115:19: warning: array subscript is of type 'char' [-Wchar-subscripts] uchar z = encode[' ']; ^~~~ 1 warning generated. In file included from Alignment.cc:3: In file included from ./Alignment.hh:8: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct In file included from Alignment.cc:4: In file included from ./Centroid.hh:6: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./Alignment.hh:15:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct 2 warnings generated. In file included from XdropAligner.cc:4: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from XdropAligner.cc:5: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from AlignmentPot.cc:3: In file included from ./AlignmentPot.hh:8: In file included from ./Alignment.hh:8: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 1 warning generated. In file included from Centroid.cc:3: In file included from ./Centroid.hh:6: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from Centroid.cc:3: In file included from ./Centroid.hh:7: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from GeneticCode.cc:4: ./Alphabet.hh:19:1: warning: 'Alphabet' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Alphabet{ ^ ./GeneticCode.hh:13:1: note: did you mean struct here? class Alphabet; ^~~~~ struct 1 warning generated. In file included from Xdrop3FrameAligner.cc:5: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from Xdrop3FrameAligner.cc:6: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from AlignmentWrite.cc:3: In file included from ./Alignment.hh:8: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct In file included from AlignmentWrite.cc:6: ./Alphabet.hh:19:1: warning: 'Alphabet' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Alphabet{ ^ ./GeneticCode.hh:13:1: note: did you mean struct here? class Alphabet; ^~~~~ struct ./Alignment.hh:17:1: note: did you mean struct here? class Alphabet; ^~~~~ struct 2 warnings generated. MultiSequenceQual.cc:191:48: warning: array subscript is of type 'char' [-Wchar-subscripts] unsigned delimiterColumn = lettersToNumbers[' ']; ^~~~ 1 warning generated. In file included from XdropAlignerPssm.cc:4: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from XdropAlignerPssm.cc:5: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from lastal.cc:13: In file included from ./Centroid.hh:6: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from lastal.cc:13: In file included from ./Centroid.hh:7: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct In file included from lastal.cc:15: In file included from ./AlignmentPot.hh:8: ./Alignment.hh:15:1: warning: class 'GeneralizedAffineGapCosts' was previously declared as a struct [-Wmismatched-tags] class GeneralizedAffineGapCosts; ^ ./GeneralizedAffineGapCosts.hh:18:8: note: previous use is here struct GeneralizedAffineGapCosts{ ^ ./Alignment.hh:15:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from lastal.cc:20: ./Alphabet.hh:19:1: warning: 'Alphabet' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Alphabet{ ^ ./Alignment.hh:17:1: note: did you mean struct here? class Alphabet; ^~~~~ struct ./GeneticCode.hh:13:1: note: did you mean struct here? class Alphabet; ^~~~~ struct 4 warnings generated. g++ -Igumbel_params -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -o lastex Alphabet.cc LastexArguments.cc io.cc ScoreMatrix.cc lastex.cc gumbel_params/*.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' ScoreMatrix.cc:115:19: warning: array subscript is of type 'char' [-Wchar-subscripts] uchar z = encode[' ']; ^~~~ 1 warning generated. In file included from lastex.cc:7: In file included from ./gumbel_params/mcf_local_alignment_evaluer.hpp:10: In file included from gumbel_params/sls_pvalues.hpp:52: gumbel_params/sls_normal_distr_array.hpp:47:15: warning: unused variable 'normal_distr_array_for_P_values_calculation' [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^ 1 warning generated. In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:3: In file included from gumbel_params/mcf_local_alignment_evaluer.hpp:10: In file included from gumbel_params/sls_pvalues.hpp:45: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:6: In file included from gumbel_params/sls_alp_sim.hpp:51: gumbel_params/sls_alp_data.hpp:515:35: warning: explicitly assigning a variable of type 'Int4' (aka 'int') to itself [-Wself-assign] v2=v2; ~~^~~ In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:3: In file included from gumbel_params/mcf_local_alignment_evaluer.hpp:10: In file included from gumbel_params/sls_pvalues.hpp:52: gumbel_params/sls_normal_distr_array.hpp:47:15: warning: unused variable 'normal_distr_array_for_P_values_calculation' [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^ In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:6: In file included from gumbel_params/sls_alp_sim.hpp:51: gumbel_params/sls_alp_data.hpp:74:21: warning: unused variable 'small_long' [-Wunused-variable] static Int4 small_long=(Int4)((double)kMin_I4/2.0); ^ 4 warnings generated. In file included from gumbel_params/njn_dynprogprob.cpp:43: In file included from gumbel_params/njn_dynprogprob.hpp:43: In file included from gumbel_params/njn_dynprogprobproto.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ gumbel_params/njn_dynprogprob.cpp:214:12: warning: unused variable 'arrayPos' [-Wunused-variable] size_t arrayPos = 0; ^ 2 warnings generated. In file included from gumbel_params/njn_dynprogproblim.cpp:39: In file included from gumbel_params/njn_dynprogproblim.hpp:42: In file included from gumbel_params/njn_dynprogprob.hpp:43: In file included from gumbel_params/njn_dynprogprobproto.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_dynprogproblim.cpp:39: gumbel_params/njn_dynprogproblim.hpp:101:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy (const DynProgProbLim &dynProgProbLim_) ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_dynprogproblim.cpp:39: gumbel_params/njn_dynprogproblim.hpp:106:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy ( ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ gumbel_params/njn_dynprogproblim.cpp:157:12: warning: unused variable 'arrayPos' [-Wunused-variable] size_t arrayPos = 0; ^ 4 warnings generated. In file included from gumbel_params/njn_dynprogprobproto.cpp:38: In file included from gumbel_params/njn_dynprogprobproto.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ 1 warning generated. In file included from gumbel_params/njn_localmaxstat.cpp:38: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_localmaxstat.cpp:40: gumbel_params/sls_alp_data.hpp:515:35: warning: explicitly assigning a variable of type 'Int4' (aka 'int') to itself [-Wself-assign] v2=v2; ~~^~~ In file included from gumbel_params/njn_localmaxstat.cpp:43: gumbel_params/njn_dynprogproblim.hpp:101:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy (const DynProgProbLim &dynProgProbLim_) ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstat.cpp:43: gumbel_params/njn_dynprogproblim.hpp:106:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy ( ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstat.cpp:46: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:46: gumbel_params/njn_vector.hpp:240:14: warning: unused variable 'i' [-Wunused-variable] size_t i = 0; ^ gumbel_params/njn_localmaxstat.cpp:154:12: warning: unused variable 'j' [-Wunused-variable] size_t j = 0; ^ gumbel_params/njn_localmaxstat.cpp:155:10: warning: unused variable 'iter' [-Wunused-variable] Int4 iter = 0; ^ gumbel_params/njn_localmaxstat.cpp:156:10: warning: unused variable 'value' [-Wunused-variable] Int4 value = 0; ^ In file included from gumbel_params/njn_localmaxstat.cpp:40: gumbel_params/sls_alp_data.hpp:74:21: warning: unused variable 'small_long' [-Wunused-variable] static Int4 small_long=(Int4)((double)kMin_I4/2.0); ^ 9 warnings generated. In file included from gumbel_params/njn_localmaxstatmatrix.cpp:38: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_localmaxstatmatrix.cpp:41: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:46: gumbel_params/njn_vector.hpp:240:14: warning: unused variable 'i' [-Wunused-variable] size_t i = 0; ^ gumbel_params/njn_localmaxstatmatrix.cpp:147:12: warning: unused variable 'j' [-Wunused-variable] size_t j = 0; ^ 3 warnings generated. In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:46: gumbel_params/njn_vector.hpp:240:14: warning: unused variable 'i' [-Wunused-variable] size_t i = 0; ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:40: gumbel_params/njn_dynprogproblim.hpp:101:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy (const DynProgProbLim &dynProgProbLim_) ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:40: gumbel_params/njn_dynprogproblim.hpp:106:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy ( ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:45: gumbel_params/sls_alp_data.hpp:515:35: warning: explicitly assigning a variable of type 'Int4' (aka 'int') to itself [-Wself-assign] v2=v2; ~~^~~ In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:43: gumbel_params/njn_approx.hpp:72:70: error: call to function 'fabs' that is neither visible in the template definition nor found by argument-dependent lookup template bool approx (T x_, T y_, T eps_) {return fabs (x_ - y_) <= fabs (eps_);} ^ gumbel_params/njn_approx.hpp:74:85: note: in instantiation of function template specialization 'ncbi::blast::Njn::Approx::approx' requested here template bool absRelApprox (T x_, T y_, T tol_, T rtol_) {return approx (x_, y_, tol_) || relApprox (x_, y_, rtol_);} ^ gumbel_params/njn_root.hpp:387:25: note: in instantiation of function template specialization 'ncbi::blast::Njn::Approx::absRelApprox' requested here if (Approx::absRelApprox (p_, x, tol_, rtol_)) return x; ^ gumbel_params/njn_root.hpp:221:17: note: in instantiation of function template specialization 'ncbi::blast::Njn::Root::bisection' requested here return bisection (y_, f, ZERO, p_, q_, tol_, rtol_, itmax_); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:182:14: note: 'fabs' should be declared prior to the call site __MATHCALLX (fabs,, (_Mdouble_ __x), (__const__)); ^ /usr/include/math.h:60:26: note: expanded from: __MATHDECLX (_Mdouble_,function,suffix, args, attrib) ^ /usr/include/math.h:62:22: note: expanded from: __MATHDECL_1(type, function,suffix, args) __attribute__ (attrib); \ ^ /usr/include/math.h:65:31: note: expanded from: extern type __MATH_PRECNAME(function,suffix) args __THROW ^ /usr/include/math.h:68:42: note: expanded from: #define __MATH_PRECNAME(name,r) __CONCAT(name,r) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:80:23: note: expanded from: #define __CONCAT(x,y) x ## y ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:43: gumbel_params/njn_approx.hpp:72:88: error: call to function 'fabs' that is neither visible in the template definition nor found by argument-dependent lookup template bool approx (T x_, T y_, T eps_) {return fabs (x_ - y_) <= fabs (eps_);} ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:182:14: note: 'fabs' should be declared prior to the call site __MATHCALLX (fabs,, (_Mdouble_ __x), (__const__)); ^ /usr/include/math.h:60:26: note: expanded from: __MATHDECLX (_Mdouble_,function,suffix, args, attrib) ^ /usr/include/math.h:62:22: note: expanded from: __MATHDECL_1(type, function,suffix, args) __attribute__ (attrib); \ ^ /usr/include/math.h:65:31: note: expanded from: extern type __MATH_PRECNAME(function,suffix) args __THROW ^ /usr/include/math.h:68:42: note: expanded from: #define __MATH_PRECNAME(name,r) __CONCAT(name,r) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:80:23: note: expanded from: #define __CONCAT(x,y) x ## y ^ 5 warnings and 2 errors generated. make[1]: *** [lastex] Error 1 make[1]: Leaving directory `/build/last-align-jgfyzN/last-align-189/src' make: *** [debian/stamp-makefile-build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0109 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-52d6de43-372b-4d01-9270-7e00485fee42/build/last-align-jgfyzN Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 7304 Build-Time: 37 Distribution: lsid64b Fail-Stage: build Install-Time: 13 Job: last-align_189-1 Package: last-align Package-Time: 64 Source-Version: 189-1 Space: 7304 Status: attempted Version: 189-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0109 Build needed 00:01:04, 7304k disc space DC-Message: Failed, but took only 155.744342. 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 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 stremi-39.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ last-align 189-1 (amd64) 13 Jan 2012 01:16 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: last-align Version: 189-1 Source Version: 189-1 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 3s (5394 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'last-align' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/last-align/trunk/ Need to get 238 kB of source archives. Get:1 http://localhost/debian/ sid/main last-align 189-1 (dsc) [2040 B] Get:2 http://localhost/debian/ sid/main last-align 189-1 (tar) [228 kB] Get:3 http://localhost/debian/ sid/main last-align 189-1 (diff) [7647 B] Fetched 238 kB in 0s (15.0 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/last-align-O4uIpX/resolver-fmHbCC/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 10 not upgraded. Need to get 0 B/704 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 unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 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/lsid64b-0bb45575-283f-4035-9f27-33e23efa3d9c/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 (>= 8), cdbs, help2man (>= 1.36.4+nmu1), python-imaging 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 (>= 8), cdbs, help2man (>= 1.36.4+nmu1), python-imaging dpkg-deb: building package `sbuild-build-depends-last-align-dummy' in `/build/last-align-O4uIpX/resolver-hSNb2N/apt_archive/sbuild-build-depends-last-align-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install last-align build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libdb4.8 libexpat1 libfreetype6 libglib2.0-0 libjpeg8 liblcms1 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-imaging python-minimal python2.6 python2.6-minimal python2.7 python2.7-minimal Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc groff liblcms-utils www-browser libmail-box-perl python-doc python-tk python-imaging-doc python-imaging-dbg python2.6-doc binfmt-support python2.7-doc Recommended packages: autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libdb4.8 libexpat1 libfreetype6 libglib2.0-0 libjpeg8 liblcms1 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-imaging python-minimal python2.6 python2.6-minimal python2.7 python2.7-minimal sbuild-build-depends-last-align-dummy 0 upgraded, 36 newly installed, 0 to remove and 10 not upgraded. Need to get 22.0 MB/22.0 MB of archives. After this operation, 66.0 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libssl1.0.0 liblocale-gettext-perl libpcre3 libglib2.0-0 libxml2 libcroco3 libexpat1 libfreetype6 libunistring0 libdb4.8 bsdmainutils groff-base man-db libmagic1 file gettext-base libsqlite3-0 mime-support python2.7-minimal python2.7 python-minimal python python2.6-minimal python2.6 cdbs html2text gettext intltool-debian po-debconf debhelper help2man libjpeg8 liblcms1 python-imaging sbuild-build-depends-last-align-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-3 [1143 kB] Get:3 http://localhost/debian/ sid/main liblocale-gettext-perl amd64 1.05-7+b1 [20.4 kB] Get:4 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:5 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:6 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:7 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:8 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7.2 [139 kB] Get:9 http://localhost/debian/ sid/main libfreetype6 amd64 2.4.8-1 [442 kB] Get:10 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:11 http://localhost/debian/ sid/main libdb4.8 amd64 4.8.30-11 [694 kB] Get:12 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:13 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:14 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:15 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:16 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:17 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:18 http://localhost/debian/ sid/main libsqlite3-0 amd64 3.7.9-3 [431 kB] Get:19 http://localhost/debian/ sid/main mime-support all 3.51-1 [35.0 kB] Get:20 http://localhost/debian/ sid/main python2.7-minimal amd64 2.7.2-10 [1766 kB] Get:21 http://localhost/debian/ sid/main python2.7 amd64 2.7.2-10 [2712 kB] Get:22 http://localhost/debian/ sid/main python-minimal all 2.7.2-9 [39.8 kB] Get:23 http://localhost/debian/ sid/main python all 2.7.2-9 [176 kB] Get:24 http://localhost/debian/ sid/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:25 http://localhost/debian/ sid/main python2.6 amd64 2.6.7-4 [2483 kB] Get:26 http://localhost/debian/ sid/main cdbs all 0.4.100 [77.1 kB] Get:27 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:28 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:29 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:30 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:31 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:32 http://localhost/debian/ sid/main help2man amd64 1.40.5 [95.6 kB] Get:33 http://localhost/debian/ sid/main libjpeg8 amd64 8c-2 [132 kB] Get:34 http://localhost/debian/ sid/main liblcms1 amd64 1.19.dfsg-1+b1 [112 kB] Get:35 http://localhost/debian/ sid/main python-imaging amd64 1.1.7-4 [457 kB] Extracting templates from packages: 83% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 22.0 MB in 0s (42.8 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_amd64.deb) ... Selecting previously unselected package liblocale-gettext-perl. Unpacking liblocale-gettext-perl (from .../liblocale-gettext-perl_1.05-7+b1_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... 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Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 clang_3.0-5 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 help2man_1.40.5 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libfreetype6_2.4.8-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 libjpeg8_8c-2 liblcms1_1.19.dfsg-1+b1 libllvm3.0_3.0-5 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-3 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-imaging_1.1.7-4 python-minimal_2.7.2-9 python2.6_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_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 Sat Oct 22 11:39:21 2011 CEST using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./last-align_189-1.dsc dpkg-source: info: extracting last-align in last-align-189 dpkg-source: info: unpacking last-align_189.orig.tar.xz dpkg-source: info: unpacking last-align_189-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package last-align dpkg-buildpackage: source version 189-1 dpkg-source --before-build last-align-189 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean make[1]: *** No rule to make target `clean'. make[1]: Entering directory `/build/last-align-O4uIpX/last-align-189' make[1]: Leaving directory `/build/last-align-O4uIpX/last-align-189' make: [makefile-clean] Error 2 (ignored) dh_clean rm -f src/lastdb src/lastal src/lastex src/*.o dpkg-source -b last-align-189 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building last-align using existing ./last-align_189.orig.tar.xz dpkg-source: info: building last-align in last-align_189-1.debian.tar.gz dpkg-source: info: building last-align in last-align_189-1.dsc debian/rules build test -x debian/rules mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" --directory src make[1]: Entering directory `/build/last-align-O4uIpX/last-align-189/src' g++ -Wall -W -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -o lastdb Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc SubsetSuffixArraySort.cc MultiSequenceQual.cc lastdb.cc clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' MultiSequenceQual.cc:191:48: warning: array subscript is of type 'char' [-Wchar-subscripts] unsigned delimiterColumn = lettersToNumbers[' ']; ^~~~ 1 warning generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c CA_code/lambda_calculator.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from CA_code/lambda_calculator.c:12: CA_code/nrutil.c:207:37: warning: incompatible pointer types passing 'int **' to parameter of type 'double **' [-Wincompatible-pointer-types] for(i=n1h;i>=n1l;i--) free_dmatrix(m[i],n2l,n2h,n3l,n3h); ^~~~ 1 warning generated. g++ -Wall -W -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -o lastal Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastalArguments.cc io.cc fileMap.cc ScoreMatrix.cc DiagonalTable.cc SegmentPair.cc Alignment.cc XdropAligner.cc SegmentPairPot.cc AlignmentPot.cc GeneralizedAffineGapCosts.cc Centroid.cc LambdaCalculator.cc TwoQualityScoreMatrix.cc OneQualityScoreMatrix.cc QualityPssmMaker.cc GeneticCode.cc Xdrop3FrameAligner.cc gaplessXdrop.cc gaplessPssmXdrop.cc gaplessTwoQualityXdrop.cc AlignmentWrite.cc MultiSequenceQual.cc XdropAlignerPssm.cc lastal.cc lambda_calculator.o clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' ScoreMatrix.cc:115:19: warning: array subscript is of type 'char' [-Wchar-subscripts] uchar z = encode[' ']; ^~~~ 1 warning generated. In file included from Alignment.cc:3: In file included from ./Alignment.hh:8: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct In file included from Alignment.cc:4: In file included from ./Centroid.hh:6: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./Alignment.hh:15:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct 2 warnings generated. In file included from XdropAligner.cc:4: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from XdropAligner.cc:5: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from AlignmentPot.cc:3: In file included from ./AlignmentPot.hh:8: In file included from ./Alignment.hh:8: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 1 warning generated. In file included from Centroid.cc:3: In file included from ./Centroid.hh:6: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from Centroid.cc:3: In file included from ./Centroid.hh:7: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from GeneticCode.cc:4: ./Alphabet.hh:19:1: warning: 'Alphabet' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Alphabet{ ^ ./GeneticCode.hh:13:1: note: did you mean struct here? class Alphabet; ^~~~~ struct 1 warning generated. In file included from Xdrop3FrameAligner.cc:5: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from Xdrop3FrameAligner.cc:6: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from AlignmentWrite.cc:3: In file included from ./Alignment.hh:8: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct In file included from AlignmentWrite.cc:6: ./Alphabet.hh:19:1: warning: 'Alphabet' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Alphabet{ ^ ./GeneticCode.hh:13:1: note: did you mean struct here? class Alphabet; ^~~~~ struct ./Alignment.hh:17:1: note: did you mean struct here? class Alphabet; ^~~~~ struct 2 warnings generated. MultiSequenceQual.cc:191:48: warning: array subscript is of type 'char' [-Wchar-subscripts] unsigned delimiterColumn = lettersToNumbers[' ']; ^~~~ 1 warning generated. In file included from XdropAlignerPssm.cc:4: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from XdropAlignerPssm.cc:5: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct 2 warnings generated. In file included from lastal.cc:13: In file included from ./Centroid.hh:6: ./GeneralizedAffineGapCosts.hh:18:1: warning: 'GeneralizedAffineGapCosts' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct GeneralizedAffineGapCosts{ ^ ./XdropAligner.hh:19:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from lastal.cc:13: In file included from ./Centroid.hh:7: ./SegmentPair.hh:11:1: warning: 'SegmentPair' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct SegmentPair{ ^ ./XdropAligner.hh:20:1: note: did you mean struct here? class SegmentPair; ^~~~~ struct In file included from lastal.cc:15: In file included from ./AlignmentPot.hh:8: ./Alignment.hh:15:1: warning: class 'GeneralizedAffineGapCosts' was previously declared as a struct [-Wmismatched-tags] class GeneralizedAffineGapCosts; ^ ./GeneralizedAffineGapCosts.hh:18:8: note: previous use is here struct GeneralizedAffineGapCosts{ ^ ./Alignment.hh:15:1: note: did you mean struct here? class GeneralizedAffineGapCosts; ^~~~~ struct In file included from lastal.cc:20: ./Alphabet.hh:19:1: warning: 'Alphabet' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Alphabet{ ^ ./Alignment.hh:17:1: note: did you mean struct here? class Alphabet; ^~~~~ struct ./GeneticCode.hh:13:1: note: did you mean struct here? class Alphabet; ^~~~~ struct 4 warnings generated. g++ -Igumbel_params -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -o lastex Alphabet.cc LastexArguments.cc io.cc ScoreMatrix.cc lastex.cc gumbel_params/*.cpp clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' ScoreMatrix.cc:115:19: warning: array subscript is of type 'char' [-Wchar-subscripts] uchar z = encode[' ']; ^~~~ 1 warning generated. In file included from lastex.cc:7: In file included from ./gumbel_params/mcf_local_alignment_evaluer.hpp:10: In file included from gumbel_params/sls_pvalues.hpp:52: gumbel_params/sls_normal_distr_array.hpp:47:15: warning: unused variable 'normal_distr_array_for_P_values_calculation' [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^ 1 warning generated. In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:3: In file included from gumbel_params/mcf_local_alignment_evaluer.hpp:10: In file included from gumbel_params/sls_pvalues.hpp:45: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:6: In file included from gumbel_params/sls_alp_sim.hpp:51: gumbel_params/sls_alp_data.hpp:515:35: warning: explicitly assigning a variable of type 'Int4' (aka 'int') to itself [-Wself-assign] v2=v2; ~~^~~ In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:3: In file included from gumbel_params/mcf_local_alignment_evaluer.hpp:10: In file included from gumbel_params/sls_pvalues.hpp:52: gumbel_params/sls_normal_distr_array.hpp:47:15: warning: unused variable 'normal_distr_array_for_P_values_calculation' [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^ In file included from gumbel_params/mcf_local_alignment_evaluer.cpp:6: In file included from gumbel_params/sls_alp_sim.hpp:51: gumbel_params/sls_alp_data.hpp:74:21: warning: unused variable 'small_long' [-Wunused-variable] static Int4 small_long=(Int4)((double)kMin_I4/2.0); ^ 4 warnings generated. In file included from gumbel_params/njn_dynprogprob.cpp:43: In file included from gumbel_params/njn_dynprogprob.hpp:43: In file included from gumbel_params/njn_dynprogprobproto.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ gumbel_params/njn_dynprogprob.cpp:214:12: warning: unused variable 'arrayPos' [-Wunused-variable] size_t arrayPos = 0; ^ 2 warnings generated. In file included from gumbel_params/njn_dynprogproblim.cpp:39: In file included from gumbel_params/njn_dynprogproblim.hpp:42: In file included from gumbel_params/njn_dynprogprob.hpp:43: In file included from gumbel_params/njn_dynprogprobproto.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_dynprogproblim.cpp:39: gumbel_params/njn_dynprogproblim.hpp:101:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy (const DynProgProbLim &dynProgProbLim_) ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_dynprogproblim.cpp:39: gumbel_params/njn_dynprogproblim.hpp:106:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy ( ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ gumbel_params/njn_dynprogproblim.cpp:157:12: warning: unused variable 'arrayPos' [-Wunused-variable] size_t arrayPos = 0; ^ 4 warnings generated. In file included from gumbel_params/njn_dynprogprobproto.cpp:38: In file included from gumbel_params/njn_dynprogprobproto.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ 1 warning generated. In file included from gumbel_params/njn_localmaxstat.cpp:38: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_localmaxstat.cpp:40: gumbel_params/sls_alp_data.hpp:515:35: warning: explicitly assigning a variable of type 'Int4' (aka 'int') to itself [-Wself-assign] v2=v2; ~~^~~ In file included from gumbel_params/njn_localmaxstat.cpp:43: gumbel_params/njn_dynprogproblim.hpp:101:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy (const DynProgProbLim &dynProgProbLim_) ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstat.cpp:43: gumbel_params/njn_dynprogproblim.hpp:106:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy ( ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstat.cpp:46: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:46: gumbel_params/njn_vector.hpp:240:14: warning: unused variable 'i' [-Wunused-variable] size_t i = 0; ^ gumbel_params/njn_localmaxstat.cpp:154:12: warning: unused variable 'j' [-Wunused-variable] size_t j = 0; ^ gumbel_params/njn_localmaxstat.cpp:155:10: warning: unused variable 'iter' [-Wunused-variable] Int4 iter = 0; ^ gumbel_params/njn_localmaxstat.cpp:156:10: warning: unused variable 'value' [-Wunused-variable] Int4 value = 0; ^ In file included from gumbel_params/njn_localmaxstat.cpp:40: gumbel_params/sls_alp_data.hpp:74:21: warning: unused variable 'small_long' [-Wunused-variable] static Int4 small_long=(Int4)((double)kMin_I4/2.0); ^ 9 warnings generated. In file included from gumbel_params/njn_localmaxstatmatrix.cpp:38: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_localmaxstatmatrix.cpp:41: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:46: gumbel_params/njn_vector.hpp:240:14: warning: unused variable 'i' [-Wunused-variable] size_t i = 0; ^ gumbel_params/njn_localmaxstatmatrix.cpp:147:12: warning: unused variable 'j' [-Wunused-variable] size_t j = 0; ^ 3 warnings generated. In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:39: gumbel_params/corelib/ncbistl.hpp:24:53: warning: using directive refers to implicitly-defined namespace 'std' namespace NCBI_NS_NCBI { /* the fake one, +"std" */ NCBI_USING_NAMESPACE_STD; } ^ gumbel_params/corelib/ncbistl.hpp:14:50: note: expanded from: #define NCBI_USING_NAMESPACE_STD using namespace NCBI_NS_STD ^ gumbel_params/corelib/ncbistl.hpp:12:22: note: expanded from: #define NCBI_NS_STD std ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:46: gumbel_params/njn_vector.hpp:240:14: warning: unused variable 'i' [-Wunused-variable] size_t i = 0; ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:40: gumbel_params/njn_dynprogproblim.hpp:101:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy (const DynProgProbLim &dynProgProbLim_) ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:40: gumbel_params/njn_dynprogproblim.hpp:106:29: warning: 'ncbi::blast::Njn::DynProgProbLim::copy' hides overloaded virtual functions [-Woverloaded-virtual] virtual inline void copy ( ^ gumbel_params/njn_dynprogprob.hpp:122:29: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual inline void copy (const DynProgProb &dynProgProb_) ^ gumbel_params/njn_dynprogprob.hpp:130:22: note: hidden overloaded virtual function 'ncbi::blast::Njn::DynProgProb::copy' declared here virtual void copy ( ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:45: gumbel_params/sls_alp_data.hpp:515:35: warning: explicitly assigning a variable of type 'Int4' (aka 'int') to itself [-Wself-assign] v2=v2; ~~^~~ In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:43: gumbel_params/njn_approx.hpp:72:70: error: call to function 'fabs' that is neither visible in the template definition nor found by argument-dependent lookup template bool approx (T x_, T y_, T eps_) {return fabs (x_ - y_) <= fabs (eps_);} ^ gumbel_params/njn_approx.hpp:74:85: note: in instantiation of function template specialization 'ncbi::blast::Njn::Approx::approx' requested here template bool absRelApprox (T x_, T y_, T tol_, T rtol_) {return approx (x_, y_, tol_) || relApprox (x_, y_, rtol_);} ^ gumbel_params/njn_root.hpp:387:25: note: in instantiation of function template specialization 'ncbi::blast::Njn::Approx::absRelApprox' requested here if (Approx::absRelApprox (p_, x, tol_, rtol_)) return x; ^ gumbel_params/njn_root.hpp:221:17: note: in instantiation of function template specialization 'ncbi::blast::Njn::Root::bisection' requested here return bisection (y_, f, ZERO, p_, q_, tol_, rtol_, itmax_); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:182:14: note: 'fabs' should be declared prior to the call site __MATHCALLX (fabs,, (_Mdouble_ __x), (__const__)); ^ /usr/include/math.h:60:26: note: expanded from: __MATHDECLX (_Mdouble_,function,suffix, args, attrib) ^ /usr/include/math.h:62:22: note: expanded from: __MATHDECL_1(type, function,suffix, args) __attribute__ (attrib); \ ^ /usr/include/math.h:65:31: note: expanded from: extern type __MATH_PRECNAME(function,suffix) args __THROW ^ /usr/include/math.h:68:42: note: expanded from: #define __MATH_PRECNAME(name,r) __CONCAT(name,r) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:80:23: note: expanded from: #define __CONCAT(x,y) x ## y ^ In file included from gumbel_params/njn_localmaxstatutil.cpp:38: In file included from gumbel_params/njn_localmaxstatutil.hpp:43: In file included from gumbel_params/njn_matrix.hpp:43: gumbel_params/njn_approx.hpp:72:88: error: call to function 'fabs' that is neither visible in the template definition nor found by argument-dependent lookup template bool approx (T x_, T y_, T eps_) {return fabs (x_ - y_) <= fabs (eps_);} ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:182:14: note: 'fabs' should be declared prior to the call site __MATHCALLX (fabs,, (_Mdouble_ __x), (__const__)); ^ /usr/include/math.h:60:26: note: expanded from: __MATHDECLX (_Mdouble_,function,suffix, args, attrib) ^ /usr/include/math.h:62:22: note: expanded from: __MATHDECL_1(type, function,suffix, args) __attribute__ (attrib); \ ^ /usr/include/math.h:65:31: note: expanded from: extern type __MATH_PRECNAME(function,suffix) args __THROW ^ /usr/include/math.h:68:42: note: expanded from: #define __MATH_PRECNAME(name,r) __CONCAT(name,r) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:80:23: note: expanded from: #define __CONCAT(x,y) x ## y ^ 5 warnings and 2 errors generated. make[1]: *** [lastex] Error 1 make[1]: Leaving directory `/build/last-align-O4uIpX/last-align-189/src' make: *** [debian/stamp-makefile-build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0117 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-0bb45575-283f-4035-9f27-33e23efa3d9c/build/last-align-O4uIpX Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 7304 Build-Time: 36 Distribution: lsid64b Fail-Stage: build Install-Time: 13 Job: last-align_189-1 Package: last-align Package-Time: 61 Source-Version: 189-1 Space: 7304 Status: attempted Version: 189-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0117 Build needed 00:01:01, 7304k disc space DC-Build-Status: Failed 608.776004s ### Content of /var/log/daemon.log ### Jan 12 21:03:53 stremi-39 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:15 stremi-39 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:16 stremi-39 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long Jan 12 21:04:21 stremi-39 approx: Concurrent download of debian/dists/sid/Release is taking too long Jan 12 21:04:31 stremi-39 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:39 stremi-39 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Jan 12 21:04:43 stremi-39 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:05:10 stremi-39 approx: Concurrent download of debian/dists/sid/Release is taking too long Jan 12 21:05:21 stremi-39 approx: Concurrent download of debian/dists/sid/Release is taking too long Jan 12 21:05:46 stremi-39 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Jan 12 21:06:02 stremi-39 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long Jan 12 21:06:13 stremi-39 approx: Concurrent download of debian/dists/sid/main/source/Sources.xz is taking too long Jan 12 21:06:26 stremi-39 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: 608.776004 versus expected 71 (r/m: 7.57430991549296 ; m: 71.0) DC-Build-Network: USED. See /tmp/rulesafter.2GJB6O ! ************************************************************ # Generated by iptables-save v1.4.8 on Fri Jan 13 01:17:09 2012 *filter :INPUT ACCEPT [4490056:37175311317] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [2531698:32150481336] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [462262:160805457] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT [31191:4148428] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [62:3720] -A OUTPUT -j LD [62:3720] -A LD -j LOG [62:3720] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Fri Jan 13 01:17:09 2012 ************************************************************ --- /tmp/rulesbefore.5o0Zu7 2012-01-13 01:07:01.045472284 +0100 +++ /tmp/rulesafter.2GJB6O 2012-01-13 01:17:09.829478645 +0100 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Fri Jan 13 01:07:01 2012 +# Generated by iptables-save v1.4.8 on Fri Jan 13 01:17:09 2012 *filter -:INPUT ACCEPT [4281546:35344128221] +:INPUT ACCEPT [4490056:37175311317] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[2398936:30421620545] -A OUTPUT -o lo -j ACCEPT +[2531698:32150481336] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,11 +16,11 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[447342:154387826] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[462262:160805457] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT -[29907:3975860] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT -[46:2760] -A OUTPUT -j LD -[46:2760] -A LD -j LOG -[46:2760] -A LD -j REJECT --reject-with icmp-port-unreachable +[31191:4148428] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[62:3720] -A OUTPUT -j LD +[62:3720] -A LD -j LOG +[62:3720] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Fri Jan 13 01:07:01 2012 +# Completed on Fri Jan 13 01:17:09 2012 ************************************************************ [ 9602.187184] IN= OUT=eth0 SRC=172.16.160.39 DST=216.62.213.249 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37281 DF PROTO=TCP SPT=56401 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 9605.204034] IN= OUT=eth0 SRC=172.16.160.39 DST=216.62.213.249 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37282 DF PROTO=TCP SPT=56401 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 9739.757773] argument2[6091]: segfault at 1f ip 00002ac470b11038 sp 00007fff520743d0 error 4 in libc-2.13.so[2ac470acd000+17a000] [ 9739.773736] argument2[6095]: segfault at 2000 ip 00002b5e46bf2038 sp 00007fff182ad7c0 error 4 in libc-2.13.so[2b5e46bae000+17a000] [ 9906.411216] IN= OUT=eth0 SRC=172.16.160.39 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=59736 DF PROTO=TCP SPT=59786 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 9916.205299] IN= OUT=eth0 SRC=172.16.160.39 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17525 DF PROTO=TCP SPT=53556 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 9929.132875] IN= OUT=eth0 SRC=172.16.160.39 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=23162 DF PROTO=TCP SPT=38865 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11622.954314] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=36131 DF PROTO=TCP SPT=41856 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11625.969703] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=36132 DF PROTO=TCP SPT=41856 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11671.087447] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26197 DF PROTO=TCP SPT=41857 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11674.104034] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26198 DF PROTO=TCP SPT=41857 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11674.142778] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=62268 DF PROTO=TCP SPT=41858 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11677.160031] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=62269 DF PROTO=TCP SPT=41858 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11677.198389] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=21021 DF PROTO=TCP SPT=41859 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11680.216030] IN= OUT=eth0 SRC=172.16.160.39 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=21022 DF PROTO=TCP SPT=41859 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11680.363011] IN= OUT=eth0 SRC=172.16.160.39 DST=193.62.193.81 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=39454 DF PROTO=TCP SPT=48233 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11683.380031] IN= OUT=eth0 SRC=172.16.160.39 DST=193.62.193.81 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=39455 DF PROTO=TCP SPT=48233 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11683.403829] IN= OUT=eth0 SRC=172.16.160.39 DST=130.223.128.45 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17103 DF PROTO=TCP SPT=42554 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11686.420035] IN= OUT=eth0 SRC=172.16.160.39 DST=130.223.128.45 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17104 DF PROTO=TCP SPT=42554 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11686.437239] IN= OUT=eth0 SRC=172.16.160.39 DST=141.161.180.205 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=19838 DF PROTO=TCP SPT=45094 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11689.456028] IN= OUT=eth0 SRC=172.16.160.39 DST=141.161.180.205 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=19839 DF PROTO=TCP SPT=45094 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11689.473260] IN= OUT=eth0 SRC=172.16.160.39 DST=193.62.192.81 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=15122 DF PROTO=TCP SPT=51672 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [11692.492028] IN= OUT=eth0 SRC=172.16.160.39 DST=193.62.192.81 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=15123 DF PROTO=TCP SPT=51672 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [13283.976798] IN= OUT=eth0 SRC=172.16.160.39 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=21669 DF PROTO=TCP SPT=33036 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [13286.996031] IN= OUT=eth0 SRC=172.16.160.39 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=21670 DF PROTO=TCP SPT=33036 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [13913.621505] IN= OUT=eth0 SRC=172.16.160.39 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=4152 DF PROTO=TCP SPT=55300 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14576.027291] IN= OUT=eth0 SRC=172.16.160.39 DST=192.0.32.8 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=34198 DF PROTO=TCP SPT=59678 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14579.044025] IN= OUT=eth0 SRC=172.16.160.39 DST=192.0.32.8 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=34199 DF PROTO=TCP SPT=59678 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14745.062763] IN= OUT=eth0 SRC=172.16.160.39 DST=193.51.224.40 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=839 DF PROTO=TCP SPT=48940 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14748.076041] IN= OUT=eth0 SRC=172.16.160.39 DST=193.51.224.40 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=840 DF PROTO=TCP SPT=48940 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14762.957224] IN= OUT=eth0 SRC=172.16.160.39 DST=193.51.224.42 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=48491 DF PROTO=TCP SPT=50201 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14765.972042] IN= OUT=eth0 SRC=172.16.160.39 DST=193.51.224.42 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=48492 DF PROTO=TCP SPT=50201 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14778.189277] IN= OUT=eth0 SRC=172.16.160.39 DST=193.51.224.40 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26645 DF PROTO=TCP SPT=48944 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [14781.208022] IN= OUT=eth0 SRC=172.16.160.39 DST=193.51.224.40 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26646 DF PROTO=TCP SPT=48944 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15316.363979] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=5923 DF PROTO=TCP SPT=52789 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15319.380032] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=5924 DF PROTO=TCP SPT=52789 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15319.399793] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=15529 DF PROTO=TCP SPT=52790 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15322.420030] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=15530 DF PROTO=TCP SPT=52790 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15322.588110] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=1393 DF PROTO=TCP SPT=52791 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15325.608032] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=1394 DF PROTO=TCP SPT=52791 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15325.626603] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=5970 DF PROTO=TCP SPT=52792 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15328.640038] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=5971 DF PROTO=TCP SPT=52792 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15328.659310] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17518 DF PROTO=TCP SPT=52793 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15331.672022] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17519 DF PROTO=TCP SPT=52793 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15331.695068] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=33633 DF PROTO=TCP SPT=52794 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15334.712114] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=33634 DF PROTO=TCP SPT=52794 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15334.731174] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=1670 DF PROTO=TCP SPT=52795 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15337.748024] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=1671 DF PROTO=TCP SPT=52795 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15337.766623] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=13942 DF PROTO=TCP SPT=52796 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [15340.784021] IN= OUT=eth0 SRC=172.16.160.39 DST=18.9.22.69 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=13943 DF PROTO=TCP SPT=52796 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 ************************************************************