sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build03.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ last-align 199-1 (armhf) 18 May 2012 15:03 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: last-align Version: 199-1 Source Version: 199-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/last-align-Zd3Z1J/last-align-199' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/last-align-Zd3Z1J' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-75b58ecc-266b-4f46-8701-bb6807bdbb06' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://repo.raspbian.lan testing InRelease [3588 B] Get:2 http://repo.raspbian.lan testing/main Sources [5945 kB] Get:3 http://repo.raspbian.lan testing/main armhf Packages [6025 kB] Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Fetched 12.0 MB in 26s (451 kB/s) Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 335 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main last-align 199-1 (dsc) [1394 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main last-align 199-1 (tar) [326 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main last-align 199-1 (diff) [7688 B] Fetched 335 kB in 0s (5237 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 `/«BUILDDIR»/resolver-XuvlU9/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 debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 20 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10672 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) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man (>= 1.36.4+nmu1), python-imaging Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man (>= 1.36.4+nmu1), python-imaging dpkg-deb: building package `sbuild-build-depends-last-align-dummy' in `/«BUILDDIR»/resolver-LW6djX/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 debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libexpat1 libffi5 libfreetype6 libglib2.0-0 libjpeg8 liblcms1 libmagic1 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-imaging python-minimal python2.7 python2.7-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff liblcms-utils less www-browser libmail-box-perl python-doc python-tk python-imaging-doc python-imaging-dbg python2.7-doc binfmt-support Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libexpat1 libffi5 libfreetype6 libglib2.0-0 libjpeg8 liblcms1 libmagic1 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-imaging python-minimal python2.7 python2.7-minimal sbuild-build-depends-last-align-dummy 0 upgraded, 32 newly installed, 0 to remove and 20 not upgraded. Need to get 414 kB/16.7 MB of archives. After this operation, 45.5 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main python-imaging armhf 1.1.7-4 [414 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 414 kB in 0s (4246 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10672 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libssl1.0.0:armhf. Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1c-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libsqlite3-0:armhf. 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Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.1) ... 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 (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7-minimal (2.7.3~rc2-2.1) ... Setting up python2.7 (2.7.3~rc2-2.1) ... Setting up python-minimal (2.7.2-10) ... Setting up python (2.7.2-10) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up help2man (1.40.9) ... Setting up liblcms1 (1.19.dfsg-1) ... Setting up python-imaging (1.1.7-4) ... Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 help2man_1.40.9 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.2-1 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libjpeg8_8d-1 liblcms1_1.19.dfsg-1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-7 libncursesw5_5.9-7 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.11-3 libss2_1.42.2-2 libssl1.0.0_1.0.1c-1 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-imaging_1.1.7-4 python-minimal_2.7.2-10 python2.7_2.7.3~rc2-2.1 python2.7-minimal_2.7.3~rc2-2.1 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-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Mon May 7 12:50:00 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./last-align_199-1.dsc dpkg-source: info: extracting last-align in last-align-199 dpkg-source: info: unpacking last-align_199.orig.tar.gz dpkg-source: info: unpacking last-align_199-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-75b58ecc-266b-4f46-8701-bb6807bdbb06 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package last-align dpkg-buildpackage: source version 199-1 dpkg-source --before-build last-align-199 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' make[2]: Entering directory `/«PKGBUILDDIR»/src' rm -f lastdb lastal lastex lambda_calculator.o make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' make all CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" make[2]: Entering directory `/«PKGBUILDDIR»' make[3]: Entering directory `/«PKGBUILDDIR»/src' if test -e ../.svn ; \ then echo \"`svnversion ..`\" | cmp -s version.hh - || echo \"`svnversion ..`\" > version.hh ; \ fi g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastdb Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc SubsetSuffixArraySort.cc MultiSequenceQual.cc lastdb.cc gcc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -c CA_code/lambda_calculator.c g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastal Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastalArguments.cc io.cc fileMap.cc ScoreMatrix.cc DiagonalTable.cc SegmentPair.cc Alignment.cc GappedXdropAligner.cc SegmentPairPot.cc AlignmentPot.cc GeneralizedAffineGapCosts.cc Centroid.cc LambdaCalculator.cc TwoQualityScoreMatrix.cc OneQualityScoreMatrix.cc QualityPssmMaker.cc GeneticCode.cc gaplessXdrop.cc gaplessPssmXdrop.cc gaplessTwoQualityXdrop.cc AlignmentWrite.cc MultiSequenceQual.cc GappedXdropAlignerPssm.cc GappedXdropAligner2qual.cc GappedXdropAligner3frame.cc lastal.cc lambda_calculator.o g++ -Igumbel_params -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastex Alphabet.cc LastexArguments.cc io.cc ScoreMatrix.cc lastex.cc gumbel_params/*.cpp gumbel_params/sls_normal_distr_array.hpp:47:15: warning: 'ncbi::blast::Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] In file included from gumbel_params/sls_alp_sim.hpp:51:0, from gumbel_params/mcf_local_alignment_evaluer.cpp:6: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] In file included from gumbel_params/sls_alp_sim.hpp:52:0, from gumbel_params/mcf_local_alignment_evaluer.cpp:6: gumbel_params/sls_alp.hpp:152:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.hpp:191:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.hpp:208:26: warning: extra ';' [-pedantic] gumbel_params/sls_normal_distr_array.hpp:47:15: warning: 'ncbi::blast::Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] gumbel_params/njn_dynprogprob.cpp: In member function 'virtual void ncbi::blast::Njn::DynProgProb::clear(Int4, Int4, const double*)': gumbel_params/njn_dynprogprob.cpp:96:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses] gumbel_params/njn_dynprogprob.cpp: In member function 'virtual void ncbi::blast::Njn::DynProgProb::update()': gumbel_params/njn_dynprogprob.cpp:214:12: warning: unused variable 'arrayPos' [-Wunused-variable] gumbel_params/njn_dynprogproblim.cpp: In member function 'virtual void ncbi::blast::Njn::DynProgProbLim::update()': gumbel_params/njn_dynprogproblim.cpp:157:12: warning: unused variable 'arrayPos' [-Wunused-variable] In file included from gumbel_params/njn_localmaxstat.cpp:40:0: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] In file included from gumbel_params/njn_localmaxstat.cpp:44:0: gumbel_params/njn_function.hpp:125:80: warning: extra ';' [-pedantic] gumbel_params/njn_localmaxstat.cpp: In member function 'void ncbi::blast::Njn::LocalMaxStat::copy(size_t, const Int4*, const double*)': gumbel_params/njn_localmaxstat.cpp:154:12: warning: unused variable 'j' [-Wunused-variable] gumbel_params/njn_localmaxstat.cpp:155:10: warning: unused variable 'iter' [-Wunused-variable] gumbel_params/njn_localmaxstat.cpp:156:10: warning: unused variable 'value' [-Wunused-variable] gumbel_params/sls_alp_data.hpp: At global scope: gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] gumbel_params/njn_localmaxstatmatrix.cpp: In member function 'void ncbi::blast::Njn::LocalMaxStatMatrix::copy(ncbi::blast::Njn::LocalMaxStat, size_t, const Int4* const*, const double*, const double*, size_t)': gumbel_params/njn_localmaxstatmatrix.cpp:147:12: warning: unused variable 'j' [-Wunused-variable] In file included from gumbel_params/njn_localmaxstatmatrix.cpp:42:0: gumbel_params/njn_memutil.hpp: At global scope: gumbel_params/njn_memutil.hpp: In instantiation of 'void ncbi::blast::Njn::MemUtil::deleteMatrix(T**&, size_t, size_t) [with T = int, size_t = unsigned int]': gumbel_params/njn_localmaxstatmatrix.cpp:67:89: instantiated from here gumbel_params/njn_memutil.hpp:111:14: warning: unused parameter 'n_' [-Wunused-parameter] gumbel_params/njn_memutil.hpp: In instantiation of 'void ncbi::blast::Njn::MemUtil::deleteMatrix(T**&, size_t, size_t) [with T = double, size_t = unsigned int]': gumbel_params/njn_localmaxstatmatrix.cpp:129:82: instantiated from here gumbel_params/njn_memutil.hpp:111:14: warning: unused parameter 'n_' [-Wunused-parameter] In file included from gumbel_params/njn_localmaxstatutil.cpp:43:0: gumbel_params/njn_root.hpp:182:13: warning: invoking macro BEGIN_SCOPE argument 1: empty macro arguments are undefined in ISO C90 and ISO C++98 [enabled by default] In file included from gumbel_params/njn_root.hpp:44:0, from gumbel_params/njn_localmaxstatutil.cpp:43: gumbel_params/njn_function.hpp:125:80: warning: extra ';' [-pedantic] In file included from gumbel_params/njn_localmaxstatutil.cpp:43:0: gumbel_params/njn_root.hpp:190:17: warning: unused parameter 'y_' [-Wunused-parameter] gumbel_params/njn_root.hpp:191:17: warning: unused parameter 'y_' [-Wunused-parameter] In file included from gumbel_params/njn_localmaxstatutil.cpp:45:0: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] In file included from gumbel_params/sls_alp.hpp:48:0, from gumbel_params/sls_alp.cpp:38: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] In file included from gumbel_params/sls_alp.cpp:38:0: gumbel_params/sls_alp.hpp:152:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.hpp:191:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.hpp:208:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:202:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:353:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:445:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:455:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:464:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp: In member function 'bool ncbi::blast::Sls::alp::one_step_of_importance_sampling_without_weight_calculation(Int4, Int4)': gumbel_params/sls_alp.cpp:470:14: warning: variable 'previous_state_' set but not used [-Wunused-but-set-variable] gumbel_params/sls_alp.cpp:474:14: warning: variable 'length1_change_' set but not used [-Wunused-but-set-variable] gumbel_params/sls_alp.cpp:475:14: warning: variable 'length2_change_' set but not used [-Wunused-but-set-variable] gumbel_params/sls_alp.cpp: At global scope: gumbel_params/sls_alp.cpp:595:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:663:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:827:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1031:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1126:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1151:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1327:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1329:6: warning: unused parameter 'ff_' [-Wunused-parameter] gumbel_params/sls_alp.cpp:1356:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp: In member function 'void ncbi::blast::Sls::alp::increment_H_weights_with_sentinels(Int4)': gumbel_params/sls_alp.cpp:1435:14: warning: unused variable 'gap_tmp' [-Wunused-variable] gumbel_params/sls_alp.cpp: At global scope: gumbel_params/sls_alp.cpp:1590:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1593:6: warning: unused parameter 'nalp_' [-Wunused-parameter] gumbel_params/sls_alp.cpp:1645:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1661:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1756:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1831:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1915:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1978:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:1992:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp.cpp:2007:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] In file included from gumbel_params/sls_alp_data.cpp:40:0: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:345:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp: In constructor 'ncbi::blast::Sls::alp_data::alp_data(Int4, Int4, Int4, std::string, std::string, std::string, double, double, double, double, std::string)': gumbel_params/sls_alp_data.cpp:468:34: warning: comparison of unsigned expression < 0 is always false [-Wtype-limits] gumbel_params/sls_alp_data.cpp: At global scope: gumbel_params/sls_alp_data.cpp:648:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:667:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:699:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:802:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:829:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:858:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:941:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1042:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1130:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1166:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1185:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1196:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1208:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1481:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1495:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.cpp:1520:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] In file included from gumbel_params/sls_alp_regression.hpp:51:0, from gumbel_params/sls_alp_regression.cpp:38: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:115:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:179:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:227:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:367:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp: In static member function 'static double ncbi::blast::Sls::alp_reg::function_for_robust_regression_sum_with_cut_LSM(double*, double*, Int4, Int4, double, double&, double&, double&, double&, bool&)': gumbel_params/sls_alp_regression.cpp:389:16: warning: unused variable 'a11_error' [-Wunused-variable] gumbel_params/sls_alp_regression.cpp:390:16: warning: unused variable 'a12_error' [-Wunused-variable] gumbel_params/sls_alp_regression.cpp:391:16: warning: unused variable 'a21_error' [-Wunused-variable] gumbel_params/sls_alp_regression.cpp:392:16: warning: unused variable 'a22_error' [-Wunused-variable] gumbel_params/sls_alp_regression.cpp: At global scope: gumbel_params/sls_alp_regression.cpp:447:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp: In static member function 'static void ncbi::blast::Sls::alp_reg::robust_regression_sum_with_cut_LSM_beta1_is_defined(Int4, Int4, double*, double*, bool, bool, double, double&, double, double&, double, Int4&, Int4&, bool&)': gumbel_params/sls_alp_regression.cpp:521:16: warning: variable 'beta1_opt' set but not used [-Wunused-but-set-variable] gumbel_params/sls_alp_regression.cpp:523:16: warning: variable 'beta1_opt_error' set but not used [-Wunused-but-set-variable] gumbel_params/sls_alp_regression.cpp: At global scope: gumbel_params/sls_alp_regression.cpp:577:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp: In static member function 'static double ncbi::blast::Sls::alp_reg::function_for_robust_regression_sum_with_cut_LSM_beta1_is_defined(double*, double*, Int4, Int4, double, double&, double, double&, double, bool&)': gumbel_params/sls_alp_regression.cpp:596:16: warning: unused variable 'a11_error' [-Wunused-variable] gumbel_params/sls_alp_regression.cpp:597:16: warning: unused variable 'a12_error' [-Wunused-variable] gumbel_params/sls_alp_regression.cpp: At global scope: gumbel_params/sls_alp_regression.cpp:646:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:658:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:675:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:723:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:745:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:747:8: warning: unused parameter 'v1_' [-Wunused-parameter] gumbel_params/sls_alp_regression.cpp:747:8: warning: unused parameter 'v2_' [-Wunused-parameter] gumbel_params/sls_alp_regression.cpp:759:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:783:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_regression.cpp:872:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] In file included from gumbel_params/sls_alp_sim.hpp:51:0, from gumbel_params/sls_alp_sim.cpp:39: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] In file included from gumbel_params/sls_alp_sim.hpp:52:0, from gumbel_params/sls_alp_sim.cpp:39: gumbel_params/sls_alp.hpp:152:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.hpp:191:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp.hpp:208:26: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp: In constructor 'ncbi::blast::Sls::alp_sim::alp_sim(ncbi::blast::Sls::alp_data*)': gumbel_params/sls_alp_sim.cpp:477:24: warning: unused variable 'memory_after2' [-Wunused-variable] gumbel_params/sls_alp_sim.cpp:724:24: warning: unused variable 'memory_after3' [-Wunused-variable] gumbel_params/sls_alp_sim.cpp: At global scope: gumbel_params/sls_alp_sim.cpp:785:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:795:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:872:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:891:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:894:6: warning: unused parameter 'time_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:894:6: warning: unused parameter 'M_min_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:1014:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1034:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1047:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1068:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1072:6: warning: unused parameter 'nalp' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:1072:6: warning: unused parameter 'C2' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:1072:6: warning: unused parameter 'C2_error' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:1072:6: warning: unused parameter 'C4' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:1072:6: warning: unused parameter 'C4_error' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:1824:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1840:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1863:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:1966:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:2027:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:2306:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:2427:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:2439:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:2441:6: warning: unused parameter 'alp_distr_errors' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:2441:6: warning: unused parameter 'lambda_error_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:3033:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3074:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3078:6: warning: unused parameter 'ind1_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:3078:6: warning: unused parameter 'ind2_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:3400:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3557:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3670:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3831:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3835:6: warning: unused parameter 'ind1_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:3835:6: warning: unused parameter 'ind2_' [-Wunused-parameter] gumbel_params/sls_alp_sim.cpp:3963:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:3989:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_sim.cpp:4172:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] In file included from gumbel_params/sls_pvalues.cpp:41:0: gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:52:8: warning: unused parameter 'v1_' [-Wunused-parameter] gumbel_params/sls_pvalues.cpp:52:8: warning: unused parameter 'v2_' [-Wunused-parameter] gumbel_params/sls_pvalues.cpp:64:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:86:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:103:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:151:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:167:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:228:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:248:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:259:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:571:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:575:6: warning: unused parameter 'P_error_' [-Wunused-parameter] gumbel_params/sls_pvalues.cpp:825:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:827:6: warning: unused parameter 'area_' [-Wunused-parameter] gumbel_params/sls_pvalues.cpp:961:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:1006:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:1012:2: warning: extra ';' [-pedantic] gumbel_params/sls_pvalues.cpp:1148:2: warning: extra ';' [-pedantic] gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable] gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable] make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' make install prefix=/«PKGBUILDDIR»/debian/last-align/usr make[2]: Entering directory `/«PKGBUILDDIR»' make[3]: Entering directory `/«PKGBUILDDIR»/src' if test -e ../.svn ; \ then echo \"`svnversion ..`\" | cmp -s version.hh - || echo \"`svnversion ..`\" > version.hh ; \ fi make[3]: Leaving directory `/«PKGBUILDDIR»/src' mkdir -p /«PKGBUILDDIR»/debian/last-align/usr/bin cp src/last?? scripts/*.?? /«PKGBUILDDIR»/debian/last-align/usr/bin make[2]: Leaving directory `/«PKGBUILDDIR»' prename 's/.py$//' debian/last-align/usr/bin/*py prename 's/.sh$//' debian/last-align/usr/bin/*sh mkdir -p /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1/ help2man --no-info --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ --version-string="199" \ /«PKGBUILDDIR»/scripts/last-dotplot.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-dotplot.1 help2man --no-info --name="genome-scale comparison of biological sequences" \ --version-string="199" --help-option="-h" \ /«PKGBUILDDIR»/src/lastal > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastal.1 help2man --no-info --name="genome-scale comparison of biological sequences" \ --version-string="199" --help-option="-h" \ /«PKGBUILDDIR»/src/lastdb > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastdb.1 help2man --no-info --name="Calculate expected numbers of alignments for random sequences." \ --version-string="199" --help-option="-h" \ /«PKGBUILDDIR»/src/lastex > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastex.1 help2man --no-info --version-string="199" \ --name="Sort MAF-format alignments by sequence name" \ /«PKGBUILDDIR»/scripts/maf-sort.sh > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-sort.1 help2man --no-info --version-string="199" \ --name="changes the order of the sequences in MAF-format alignments" \ /«PKGBUILDDIR»/scripts/maf-swap.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-swap.1 help2man --no-info --version-string="199" \ --name="Add extra column with mapping probabilities" \ /«PKGBUILDDIR»/scripts/last-map-probs.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-map-probs.1 help2man --no-info --version-string="199" \ --name="Read files of lastal output, merge corresponding batches, and write them." \ /«PKGBUILDDIR»/scripts/last-merge-batches.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-merge-batches.1 help2man --no-info --version-string="199" \ --name="Clean up MAF-format alignments" \ /«PKGBUILDDIR»/scripts/last-reduce-alignments.sh > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-reduce-alignments.1 help2man --no-info --version-string="199" \ --name='Remove MAF-format alignments which are "dominated" by others' \ /«PKGBUILDDIR»/scripts/last-remove-dominated.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-remove-dominated.1 help2man --no-info --version-string="199" \ --name="Join two or more sets of MAF-format multiple alignments" \ /«PKGBUILDDIR»/scripts/maf-join.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-join.1 help2man --no-info --version-string="199" \ --name="Convert MAF-format alignments to tabular format" \ /«PKGBUILDDIR»/scripts/maf-convert.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-convert.1 help2man --no-info --version-string="199" \ --name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \ /«PKGBUILDDIR»/scripts/maf-cull.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-cull.1 help2man --no-info --version-string="199" \ --name="Read alignments of paired DNA reads to a genome" \ /«PKGBUILDDIR»/scripts/last-pair-probs.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-pair-probs.1 make[1]: Leaving directory `/«PKGBUILDDIR»' dh_install -a dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory `/«PKGBUILDDIR»' dh_installchangelogs ChangeLog.txt make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastex contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `last-align' in `../last-align_199-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../last-align_199-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build last-align-199 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120518-1516 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ last-align_199-1_armhf.changes: ─────────────────────────────── Format: 1.8 Date: Mon, 07 May 2012 13:28:25 +0200 Source: last-align Binary: last-align Architecture: armhf Version: 199-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: last-align - genome-scale comparison of biological sequences Closes: 667939 Changes: last-align (199-1) unstable; urgency=low . [ Charles Plessy ] * Summarise LAST license in debian/copyright header. . [ Andreas Tille ] * New upstream version Closes: #667939 * debian/rules: - switch from cdbs to dh - add help2man call for lastex * debian/install: - removed to use upstream install target (which also installs lastex) * debian/copyright: Make Source field more generic Checksums-Sha1: accf18c561a165fc62c1a827ad80456a8abb8201 434828 last-align_199-1_armhf.deb Checksums-Sha256: 3b07f4fa4cc98c3d997b15c39490f8a83a224458547f7b2d445118b2fbe1d0c7 434828 last-align_199-1_armhf.deb Files: 2f152f14150fb3f3e25cade246458432 434828 science optional last-align_199-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ last-align_199-1_armhf.deb ────────────────────────── new debian package, version 2.0. size 434828 bytes: control archive= 2684 bytes. 1192 bytes, 25 lines control 4476 bytes, 63 lines md5sums Package: last-align Version: 199-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 804 Pre-Depends: dpkg (>= 1.15.6) Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0) Recommends: python, python-imaging Section: science Priority: optional Homepage: http://last.cbrc.jp/ Description: genome-scale comparison of biological sequences LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. Here are two things LAST is good at: . * Comparing large (e.g. mammalian) genomes. * Mapping lots of sequence tags onto a genome. . The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). This allows one to map tags to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. To find these variable-sized matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a discontiguous suffix array, analogous to spaced seeds. drwxr-xr-x root/root 0 2012-05-18 15:15 ./ drwxr-xr-x root/root 0 2012-05-18 15:15 ./usr/ drwxr-xr-x root/root 0 2012-05-18 15:15 ./usr/bin/ -rwxr-xr-x root/root 235428 2012-05-18 15:15 ./usr/bin/lastal -rwxr-xr-x root/root 4762 2012-05-18 15:14 ./usr/bin/maf-swap -rwxr-xr-x root/root 9590 2012-05-18 15:14 ./usr/bin/last-dotplot -rwxr-xr-x root/root 8992 2012-05-18 15:14 ./usr/bin/maf-join -rwxr-xr-x root/root 14329 2012-05-18 15:14 ./usr/bin/last-pair-probs -rwxr-xr-x root/root 4594 2012-05-18 15:14 ./usr/bin/last-map-probs -rwxr-xr-x root/root 20318 2012-05-18 15:14 ./usr/bin/maf-convert -rwxr-xr-x root/root 1117 2012-05-18 15:14 ./usr/bin/last-merge-batches -rwxr-xr-x root/root 91976 2012-05-18 15:15 ./usr/bin/lastdb -rwxr-xr-x root/root 2027 2012-05-18 15:14 ./usr/bin/maf-sort -rwxr-xr-x root/root 5992 2012-05-18 15:14 ./usr/bin/last-remove-dominated -rwxr-xr-x root/root 4266 2012-05-18 15:14 ./usr/bin/maf-cull -rwxr-xr-x root/root 239324 2012-05-18 15:15 ./usr/bin/lastex -rwxr-xr-x root/root 1187 2012-05-18 15:14 ./usr/bin/last-reduce-alignments drwxr-xr-x root/root 0 2012-05-18 15:15 ./usr/share/ drwxr-xr-x root/root 0 2012-05-18 15:15 ./usr/share/doc-base/ -rw-r--r-- root/root 486 2010-06-24 03:10 ./usr/share/doc-base/last-align-lastex -rw-r--r-- root/root 281 2011-03-11 14:35 ./usr/share/doc-base/last-align-manual -rw-r--r-- root/root 293 2010-06-24 03:10 ./usr/share/doc-base/last-align-scripts -rw-r--r-- root/root 294 2010-06-24 03:10 ./usr/share/doc-base/last-align-seeds drwxr-xr-x root/root 0 2012-05-18 15:15 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-18 15:15 ./usr/share/man/man1/ -rw-r--r-- root/root 524 2012-05-18 15:15 ./usr/share/man/man1/last-dotplot.1.gz -rw-r--r-- root/root 273 2012-05-18 15:15 ./usr/share/man/man1/maf-join.1.gz -rw-r--r-- root/root 329 2012-05-18 15:15 ./usr/share/man/man1/maf-swap.1.gz -rw-r--r-- root/root 471 2012-05-18 15:15 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└──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* file* gettext* gettext-base* groff-base* help2man* html2text* intltool-debian* libcroco3* libexpat1* libffi5* libfreetype6* libglib2.0-0* libjpeg8* liblcms1* libmagic1* libpcre3* libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2* man-db* mime-support* po-debconf* python* python-imaging* python-minimal* python2.7* python2.7-minimal* sbuild-build-depends-core-dummy* sbuild-build-depends-last-align-dummy* 0 upgraded, 0 newly installed, 33 to remove and 20 not upgraded. After this operation, 45.5 MB disk space will be freed. (Reading database ... 13270 files and directories currently installed.) Removing sbuild-build-depends-last-align-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing help2man ... Removing html2text ... Purging configuration files for html2text ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing python-imaging ... Removing python ... Purging configuration files for python ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing libexpat1:armhf ... Purging configuration files for libexpat1:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libfreetype6:armhf ... Purging configuration files for libfreetype6:armhf ... Removing libjpeg8:armhf ... Removing liblcms1 ... Purging configuration files for liblcms1 ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libsqlite3-0:armhf ... Purging configuration files for libsqlite3-0:armhf ... Removing python-minimal ... Removing python2.7-minimal ... Purging configuration files for python2.7-minimal ... Removing libssl1.0.0:armhf ... Purging configuration files for libssl1.0.0:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing mime-support ... Purging configuration files for mime-support ... Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 9384 Build-Time: 618 Distribution: testing Install-Time: 95 Job: last-align_199-1 Package: last-align Package-Time: 758 Source-Version: 199-1 Space: 9384 Status: successful Version: 199-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120518-1516 Build needed 00:12:38, 9384k disc space