last-align →
475-1 →
armhf → 2014-08-21 05:53:46
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ last-align 475-1 (armhf) 21 Aug 2014 05:40 ║
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Package: last-align
Version: 475-1
Source Version: 475-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/last-align-13lnLC/last-align-475' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/last-align-13lnLC' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-c8cec526-ef5b-4c0a-8a98-695514c7a726' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
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Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7478 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8532 kB]
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Check APT
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NOTICE: 'last-align' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/last-align/trunk/
Need to get 396 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main last-align 475-1 (dsc) [1992 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main last-align 475-1 (tar) [386 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main last-align 475-1 (diff) [7596 B]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-Rk2h4F/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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Building dependency tree...
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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 60 not upgraded.
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Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man, python-imaging
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man, python-imaging
dpkg-deb: building package `sbuild-build-depends-last-align-dummy' in `/«BUILDDIR»/resolver-e8LCpU/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
intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libfreetype6
libglib2.0-0 libjbig0 libjpeg8 liblcms2-2 libmagic1 libpipeline1 libpng12-0
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
libssl1.0.0 libtiff5 libunistring0 libwebp5 libwebpdemux1 libwebpmux1
libxml2 man-db mime-support po-debconf python python-imaging python-minimal
python-pil python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff liblcms2-utils
less www-browser libmail-box-perl python-doc python-tk python-pil-doc
python-pil-dbg python2.7-doc binfmt-support
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
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
intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libfreetype6
libglib2.0-0 libjbig0 libjpeg8 liblcms2-2 libmagic1 libpipeline1 libpng12-0
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
libssl1.0.0 libtiff5 libunistring0 libwebp5 libwebpdemux1 libwebpmux1
libxml2 man-db mime-support po-debconf python python-imaging python-minimal
python-pil python2.7 python2.7-minimal sbuild-build-depends-last-align-dummy
0 upgraded, 41 newly installed, 0 to remove and 60 not upgraded.
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Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
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Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.19.2-1 [30.5 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.19-1 [232 kB]
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Get:16 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.50-2 [160 kB]
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Get:18 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.1-3 [27.3 kB]
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Get:22 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libwebp5 armhf 0.4.0-4.1 [157 kB]
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Get:26 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.19-1 [57.7 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.19.2-1 [116 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.56 [35.5 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.8-4 [1834 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.8-4 [243 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.8-1 [39.8 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.8-1 [19.2 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.8-1 [150 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.19.2-1 [1160 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140809 [690 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.46.1 [128 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main python-pil armhf 2.4.0-2 [285 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main python-imaging all 2.5.1-1 [9110 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140617-1 dpkg-dev_1.17.10 g++-4.9_4.9.0-7 gcc-4.8_4.8.3-4 gcc-4.9_4.9.0-7 libc6-dev_2.19-7 libstdc++-4.9-dev_4.9.0-7 libstdc++6_4.9.0-7 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.6 base-files_7.3+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140617-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.0-4 cpp-4.8_4.8.3-4 cpp-4.9_4.9.0-7 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140809 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1.1 e2fsprogs_1.42.10-1.1 fakeroot_1.18.4-2 file_1:5.19-1 findutils_4.4.2-9 g++_4:4.9.0-4 g++-4.9_4.9.0-7 gcc_4:4.9.0-4 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-4 gcc-4.8-base_4.8.3-4 gcc-4.9_4.9.0-7 gcc-4.9-base_4.9.0-7 gettext_0.19.2-1 gettext-base_0.19.2-1 gnupg_1.4.18-2 gpgv_1.4.18-2 grep_2.18-2 groff-base_1.22.2-6 gzip_1.6-3 help2man_1.46.1 hostname_3.15 init-system-helpers_1.19 initramfs-tools_0.115 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.6 libasan0_4.8.3-4 libasan1_4.9.0-7 libasprintf0c2_0.19.2-1 libatomic1_4.9.0-7 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libc-bin_2.19-7 libc-dev-bin_2.19-7 libc6_2.19-7 libc6-dev_2.19-7 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.10-1.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-5 libdbus-1-3_1.8.6-1 libdpkg-perl_1.17.10 libexpat1_2.1.0-6 libffi6_3.1-2 libfreetype6_2.5.2-1.1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-4 libgcc-4.9-dev_4.9.0-7 libgcc1_1:4.9.0-7 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-4 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.0-7 libisl10_0.12.2-2 libjbig0_2.1-3 libjpeg8_8d1-1 libklibc_2.0.3-1+rpi1 libkmod2_16-2 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-8 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmount1_2.20.1-5.8 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libpng12-0_1.2.50-2 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libpython-stdlib_2.7.8-1 libpython2.7-minimal_2.7.8-4 libpython2.7-stdlib_2.7.8-4 libreadline6_6.3-6 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-17 libsqlite3-0_3.8.5-2 libss2_1.42.10-1.1 libssl1.0.0_1.0.1i-2 libstdc++-4.9-dev_4.9.0-7 libstdc++6_4.9.0-7 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtiff5_4.0.3-9 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libubsan0_4.9.0-7 libudev1_204-14 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libwebp5_0.4.0-4.1 libwebpdemux1_0.4.0-4.1 libwebpmux1_0.4.0-4.1 libxml2_2.9.1+dfsg1-4 linux-libc-dev_3.14.4-1+rpi1 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mime-support_3.56 mount_2.20.1-5.8 multiarch-support_2.19-7 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-6 perl-base_5.18.2-6 perl-modules_5.18.2-6 plymouth_0.9.0-4 po-debconf_1.0.16+nmu3 procps_1:3.3.9-5 python_2.7.8-1 python-imaging_2.5.1-1 python-minimal_2.7.8-1 python-pil_2.4.0-2 python2.7_2.7.8-4 python2.7-minimal_2.7.8-4 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 udev_204-14 util-linux_2.20.1-5.8 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Aug 16 06:31:18 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./last-align_475-1.dsc
dpkg-source: info: extracting last-align in last-align-475
dpkg-source: info: unpacking last-align_475.orig.tar.gz
dpkg-source: info: unpacking last-align_475-1.debian.tar.xz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-c8cec526-ef5b-4c0a-8a98-695514c7a726
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package last-align
dpkg-buildpackage: source version 475-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build last-align-475
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 last-split last-merge-batches *.o */*.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 -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 -Werror=format-security" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
make[2]: Entering directory '/«PKGBUILDDIR»'
make[3]: Entering directory '/«PKGBUILDDIR»/src'
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o Alphabet.o Alphabet.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o MultiSequence.o MultiSequence.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o LastdbArguments.o LastdbArguments.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o io.o io.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o fileMap.o fileMap.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc
SubsetSuffixArraySort.cc: In member function 'void cbrc::SubsetSuffixArray::sortIndex(const uchar*, cbrc::SubsetSuffixArray::indexT)':
SubsetSuffixArraySort.cc:224:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( end - beg <= maxUnsortedInterval ) continue;
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc
if test -e ../.hg ; \
then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \
elif test -e ../.hg_archival.txt ; \
then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \
else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \
fi
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o lastdb.o lastdb.cc
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastdb Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastdbArguments.o io.o fileMap.o SubsetSuffixArraySort.o MultiSequenceQual.o lastdb.o
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o LastalArguments.o LastalArguments.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o ScoreMatrix.o ScoreMatrix.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o DiagonalTable.o DiagonalTable.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o SegmentPair.o SegmentPair.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o Alignment.o Alignment.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o SegmentPairPot.o SegmentPairPot.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o AlignmentPot.o AlignmentPot.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o GeneralizedAffineGapCosts.o GeneralizedAffineGapCosts.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o Centroid.o Centroid.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o LambdaCalculator.o LambdaCalculator.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o GeneticCode.o GeneticCode.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o gaplessXdrop.o gaplessXdrop.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o AlignmentWrite.o AlignmentWrite.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o lastal.o lastal.cc
gcc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o CA_code/lambda_calculator.o CA_code/lambda_calculator.c
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastal Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastalArguments.o io.o fileMap.o ScoreMatrix.o DiagonalTable.o SegmentPair.o Alignment.o GappedXdropAligner.o SegmentPairPot.o AlignmentPot.o GeneralizedAffineGapCosts.o Centroid.o LambdaCalculator.o TwoQualityScoreMatrix.o OneQualityScoreMatrix.o QualityPssmMaker.o GeneticCode.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o AlignmentWrite.o MultiSequenceQual.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o lastal.o CA_code/lambda_calculator.o
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o LastexArguments.o LastexArguments.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o lastex.o lastex.cc
In file included from gumbel_params/sls_pvalues.hpp:52:0,
from gumbel_params/mcf_local_alignment_evaluer.hpp:10,
from lastex.cc:7:
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]
static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/mcf_local_alignment_evaluer.o gumbel_params/mcf_local_alignment_evaluer.cpp
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 ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
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 ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.hpp:191:26: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.hpp:208:26: warning: extra ';' [-Wpedantic]
};
^
In file included from gumbel_params/sls_pvalues.hpp:52:0,
from gumbel_params/mcf_local_alignment_evaluer.hpp:10,
from gumbel_params/mcf_local_alignment_evaluer.cpp:3:
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]
static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={
^
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:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_dynprogprob.o gumbel_params/njn_dynprogprob.cpp
In file included from gumbel_params/njn_dynprogprob.cpp:41:0:
gumbel_params/njn_dynprogprob.cpp: In member function 'virtual void ncbi::blast::Njn::DynProgProb::clear(Int4, Int4, const double*)':
gumbel_params/njn_dynprogprob.cpp:97:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
prob_ && valueLower_ < valueUpper_);
^
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]
size_t arrayPos = 0;
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_dynprogproblim.o gumbel_params/njn_dynprogproblim.cpp
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]
size_t arrayPos = 0;
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_dynprogprobproto.o gumbel_params/njn_dynprogprobproto.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_ioutil.o gumbel_params/njn_ioutil.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_localmaxstat.o gumbel_params/njn_localmaxstat.cpp
In file included from gumbel_params/njn_localmaxstat.cpp:40:0:
gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
In file included from gumbel_params/njn_localmaxstat.cpp:44:0:
gumbel_params/njn_function.hpp:125:80: warning: extra ';' [-Wpedantic]
template <typename T> bool isProb (T x_) {return 0.0 <= x_ && x_ <= 1.0;}; // the closest value to x_ in the interval [0.0, 1.0]
^
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]
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:40:0:
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]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_localmaxstatmatrix.o gumbel_params/njn_localmaxstatmatrix.cpp
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]
size_t j = 0;
^
In file included from gumbel_params/njn_localmaxstatmatrix.cpp:42:0:
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: required from here
gumbel_params/njn_memutil.hpp:111:59: warning: unused parameter 'n_' [-Wunused-parameter]
void deleteMatrix (T **&matrix, size_t m_, size_t n_)
^
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: required from here
gumbel_params/njn_memutil.hpp:111:59: warning: unused parameter 'n_' [-Wunused-parameter]
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_localmaxstatutil.o gumbel_params/njn_localmaxstatutil.cpp
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
BEGIN_SCOPE()
^
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 ';' [-Wpedantic]
template <typename T> bool isProb (T x_) {return 0.0 <= x_ && x_ <= 1.0;}; // the closest value to x_ in the interval [0.0, 1.0]
^
In file included from gumbel_params/njn_localmaxstatutil.cpp:43:0:
gumbel_params/njn_root.hpp:190:45: warning: unused parameter 'y_' [-Wunused-parameter]
double f (double x_, const double &y_) {return (*s_f) (x_);}
^
gumbel_params/njn_root.hpp:191:46: warning: unused parameter 'y_' [-Wunused-parameter]
double df (double x_, const double &y_) {return (*s_df) (x_);}
^
In file included from gumbel_params/njn_localmaxstatutil.cpp:45:0:
gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/njn_matrix.o gumbel_params/njn_matrix.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/random_gen.o gumbel_params/random_gen.cpp
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/sls_alp.o gumbel_params/sls_alp.cpp
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 ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
In file included from gumbel_params/sls_alp.cpp:38:0:
gumbel_params/sls_alp.hpp:152:26: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.hpp:191:26: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.hpp:208:26: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:202:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:353:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:445:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:455:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:464:2: warning: extra ';' [-Wpedantic]
};
^
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]
char previous_state_;
^
gumbel_params/sls_alp.cpp:474:14: warning: variable 'length1_change_' set but not used [-Wunused-but-set-variable]
bool length1_change_;
^
gumbel_params/sls_alp.cpp:475:14: warning: variable 'length2_change_' set but not used [-Wunused-but-set-variable]
bool length2_change_;
^
gumbel_params/sls_alp.cpp: At global scope:
gumbel_params/sls_alp.cpp:595:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:663:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:827:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1031:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1126:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1151:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1327:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1330:6: warning: unused parameter 'ff_' [-Wunused-parameter]
Int4 ff_)
^
gumbel_params/sls_alp.cpp:1356:2: warning: extra ';' [-Wpedantic]
};
^
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]
Int4 gap_tmp=-d_alp_data->d_open-d_H_matr_len_1*d_alp_data->d_epen;
^
gumbel_params/sls_alp.cpp: At global scope:
gumbel_params/sls_alp.cpp:1590:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1594:6: warning: unused parameter 'nalp_' [-Wunused-parameter]
Int4 nalp_,
^
gumbel_params/sls_alp.cpp:1645:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1661:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1756:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1831:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1915:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1978:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:1992:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.cpp:2007:2: warning: extra ';' [-Wpedantic]
};
^
In file included from gumbel_params/sls_alp.hpp:48:0,
from gumbel_params/sls_alp.cpp:38:
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/sls_alp_data.o gumbel_params/sls_alp_data.cpp
In file included from gumbel_params/sls_alp_data.cpp:40:0:
gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:345:2: warning: extra ';' [-Wpedantic]
};
^
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:468:33: warning: comparison of unsigned expression < 0 is always false [-Wtype-limits]
if(random_factor<0)
^
gumbel_params/sls_alp_data.cpp: At global scope:
gumbel_params/sls_alp_data.cpp:648:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:667:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:699:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:802:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:829:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:858:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:941:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1042:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1130:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1166:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1185:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1196:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1208:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1481:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1495:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.cpp:1520:2: warning: extra ';' [-Wpedantic]
};
^
In file included from gumbel_params/sls_alp_data.cpp:40:0:
gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/sls_alp_regression.o gumbel_params/sls_alp_regression.cpp
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 ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:115:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:179:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:227:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:367:2: warning: extra ';' [-Wpedantic]
};
^
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]
double a11_error=0;
^
gumbel_params/sls_alp_regression.cpp:390:16: warning: unused variable 'a12_error' [-Wunused-variable]
double a12_error=0;
^
gumbel_params/sls_alp_regression.cpp:391:16: warning: unused variable 'a21_error' [-Wunused-variable]
double a21_error=0;
^
gumbel_params/sls_alp_regression.cpp:392:16: warning: unused variable 'a22_error' [-Wunused-variable]
double a22_error=0;
^
gumbel_params/sls_alp_regression.cpp: At global scope:
gumbel_params/sls_alp_regression.cpp:447:2: warning: extra ';' [-Wpedantic]
};
^
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]
double beta1_opt=beta1_;
^
gumbel_params/sls_alp_regression.cpp:523:16: warning: variable 'beta1_opt_error' set but not used [-Wunused-but-set-variable]
double beta1_opt_error=beta1_error_;
^
gumbel_params/sls_alp_regression.cpp: At global scope:
gumbel_params/sls_alp_regression.cpp:577:2: warning: extra ';' [-Wpedantic]
};
^
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]
double a11_error=0;
^
gumbel_params/sls_alp_regression.cpp:597:16: warning: unused variable 'a12_error' [-Wunused-variable]
double a12_error=0;
^
gumbel_params/sls_alp_regression.cpp: At global scope:
gumbel_params/sls_alp_regression.cpp:646:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:658:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:675:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:723:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:745:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:748:8: warning: unused parameter 'v1_' [-Wunused-parameter]
double v1_,
^
gumbel_params/sls_alp_regression.cpp:750:8: warning: unused parameter 'v2_' [-Wunused-parameter]
double v2_,
^
gumbel_params/sls_alp_regression.cpp:759:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:783:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_regression.cpp:872:2: warning: extra ';' [-Wpedantic]
};
^
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:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/sls_alp_sim.o gumbel_params/sls_alp_sim.cpp
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 ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
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 ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.hpp:191:26: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp.hpp:208:26: warning: extra ';' [-Wpedantic]
};
^
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]
double memory_after2=d_alp_data->d_memory_size_in_MB;
^
gumbel_params/sls_alp_sim.cpp:724:24: warning: unused variable 'memory_after3' [-Wunused-variable]
double memory_after3=d_alp_data->d_memory_size_in_MB;
^
gumbel_params/sls_alp_sim.cpp: At global scope:
gumbel_params/sls_alp_sim.cpp:785:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:795:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:872:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:891:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:895:8: warning: unused parameter 'time_' [-Wunused-parameter]
double time_,
^
gumbel_params/sls_alp_sim.cpp:899:6: warning: unused parameter 'M_min_' [-Wunused-parameter]
Int4 M_min_,
^
gumbel_params/sls_alp_sim.cpp:1014:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1034:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1047:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1068:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1075:6: warning: unused parameter 'nalp' [-Wunused-parameter]
Int4 nalp,
^
gumbel_params/sls_alp_sim.cpp:1085:9: warning: unused parameter 'C2' [-Wunused-parameter]
double &C2,
^
gumbel_params/sls_alp_sim.cpp:1086:9: warning: unused parameter 'C2_error' [-Wunused-parameter]
double &C2_error,
^
gumbel_params/sls_alp_sim.cpp:1087:9: warning: unused parameter 'C4' [-Wunused-parameter]
double &C4,
^
gumbel_params/sls_alp_sim.cpp:1088:9: warning: unused parameter 'C4_error' [-Wunused-parameter]
double &C4_error,
^
gumbel_params/sls_alp_sim.cpp:1824:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1840:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1863:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:1966:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:2027:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:2306:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:2427:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:2439:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:2446:8: warning: unused parameter 'alp_distr_errors' [-Wunused-parameter]
void **alp_distr_errors,
^
gumbel_params/sls_alp_sim.cpp:2448:8: warning: unused parameter 'lambda_error_' [-Wunused-parameter]
double lambda_error_,
^
gumbel_params/sls_alp_sim.cpp:3033:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3074:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3081:6: warning: unused parameter 'ind1_' [-Wunused-parameter]
Int4 ind1_,
^
gumbel_params/sls_alp_sim.cpp:3082:6: warning: unused parameter 'ind2_' [-Wunused-parameter]
Int4 ind2_,
^
gumbel_params/sls_alp_sim.cpp:3400:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3557:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3670:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3831:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3840:6: warning: unused parameter 'ind1_' [-Wunused-parameter]
Int4 ind1_,
^
gumbel_params/sls_alp_sim.cpp:3841:6: warning: unused parameter 'ind2_' [-Wunused-parameter]
Int4 ind2_,
^
gumbel_params/sls_alp_sim.cpp:3963:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:3989:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_sim.cpp:4172:2: warning: extra ';' [-Wpedantic]
};
^
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:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -c -o gumbel_params/sls_pvalues.o gumbel_params/sls_pvalues.cpp
In file included from gumbel_params/sls_pvalues.cpp:41:0:
gumbel_params/sls_alp_data.hpp:469:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:487:18: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:531:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:542:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:552:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:559:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:565:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:571:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:577:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:667:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:728:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:741:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:805:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_alp_data.hpp:866:10: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:53:8: warning: unused parameter 'v1_' [-Wunused-parameter]
double v1_,
^
gumbel_params/sls_pvalues.cpp:55:8: warning: unused parameter 'v2_' [-Wunused-parameter]
double v2_,
^
gumbel_params/sls_pvalues.cpp:64:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:86:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:103:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:151:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:167:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:228:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:248:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:259:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:571:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:583:9: warning: unused parameter 'P_error_' [-Wunused-parameter]
double &P_error_,
^
gumbel_params/sls_pvalues.cpp:825:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:837:9: warning: unused parameter 'area_' [-Wunused-parameter]
double &area_,
^
gumbel_params/sls_pvalues.cpp:961:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:1006:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:1012:2: warning: extra ';' [-Wpedantic]
};
^
gumbel_params/sls_pvalues.cpp:1148:2: warning: extra ';' [-Wpedantic]
};
^
In file included from gumbel_params/sls_pvalues.cpp:41:0:
gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
static Int4 small_long=(Int4)((double)kMin_I4/2.0);
^
gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
static double dbl_max_log=log(DBL_MAX);
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o lastex Alphabet.o LastexArguments.o io.o ScoreMatrix.o lastex.o gumbel_params/mcf_local_alignment_evaluer.o gumbel_params/njn_dynprogprob.o gumbel_params/njn_dynprogproblim.o gumbel_params/njn_dynprogprobproto.o gumbel_params/njn_ioutil.o gumbel_params/njn_localmaxstat.o gumbel_params/njn_localmaxstatmatrix.o gumbel_params/njn_localmaxstatutil.o gumbel_params/njn_matrix.o gumbel_params/random_gen.o gumbel_params/sls_alp.o gumbel_params/sls_alp_data.o gumbel_params/sls_alp_regression.o gumbel_params/sls_alp_sim.o gumbel_params/sls_pvalues.o
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o split/cbrc_linalg.o split/cbrc_linalg.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o split/last-split.o split/last-split.cc
split/last-split.cc: In function 'void doOneQuery(std::vector<cbrc::UnsplitAlignment>::const_iterator, std::vector<cbrc::UnsplitAlignment>::const_iterator, cbrc::SplitAligner&, const LastSplitOptions&)':
split/last-split.cc:140:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned i = 0; i < end - beg; ++i) {
^
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o split/last-split-main.o split/last-split-main.cc
g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Igumbel_params -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -Wl,-z,relro -o last-split Alphabet.o MultiSequence.o fileMap.o split/cbrc_linalg.o split/last-split.o split/cbrc_split_aligner.o split/last-split-main.o split/cbrc_unsplit_alignment.o
gcc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -o last-merge-batches last-merge-batches.o
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
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 ../.hg ; \
then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \
elif test -e ../.hg_archival.txt ; \
then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \
else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \
fi
make[3]: Leaving directory '/«PKGBUILDDIR»/src'
mkdir -p /«PKGBUILDDIR»/debian/last-align/usr/bin
cp src/last?? src/last-split src/last-merge-batches 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 --version-string="475" \
--name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
/«PKGBUILDDIR»/scripts/last-dotplot.py > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-dotplot.1
help2man --no-info --version-string="475" \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
/«PKGBUILDDIR»/src/lastal > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastal.1
help2man --no-info --version-string="475" \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
/«PKGBUILDDIR»/src/lastdb > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastdb.1
help2man --no-info --version-string="475" \
--name="Calculate expected numbers of alignments for random sequences." \
--help-option="-h" \
/«PKGBUILDDIR»/src/lastex > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//lastex.1
help2man --no-info --version-string="475" \
--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="475" \
--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="475" \
--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
# This script has not enough to put in a manual page.
#help2man --no-info --version-string="475" \
# --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="475" \
# --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="475" \
# --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="475" \
--name='Estimates "split" or "spliced" alignments.' \
/«PKGBUILDDIR»/src/last-split > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-split.1
help2man --no-info --version-string="475" \
--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="475" \
--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="475" \
--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="475" \
--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_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_perl -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/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `last-align' in `../last-align_475-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_475-1_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-475
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140821-0553
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_475-1_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Sat, 16 Aug 2014 15:20:37 +0900
Source: last-align
Binary: last-align
Architecture: armhf
Version: 475-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (475-1) unstable; urgency=medium
.
* New upstream release.
* debian/rules:
- removed compression command, as it is now the default.
- removed manual page of last-merge-batches.py.
* debian/control: suggest GNU parallel.
* debian/README.source: removed as conversion from zip is now automagic.
Checksums-Sha1:
6c055082256571cf6b524a928c5543b458441250 400818 last-align_475-1_armhf.deb
Checksums-Sha256:
2129330c990143cafa66ae7b7688bd45239c5fbbbef14e139bfd3d00eb2c1e81 400818 last-align_475-1_armhf.deb
Files:
da1a9c1609928dd9802763764ef18f13 400818 science optional last-align_475-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_475-1_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 400818 bytes: control archive=3077 bytes.
1176 bytes, 25 lines control
5146 bytes, 73 lines md5sums
Package: last-align
Version: 475-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1058
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.9)
Recommends: python, python-imaging
Suggests: parallel
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 2014-08-21 05:53 ./
drwxr-xr-x root/root 0 2014-08-21 05:52 ./usr/
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/bin/
-rwxr-xr-x root/root 234 2014-08-21 05:52 ./usr/bin/parallel-fasta
-rwxr-xr-x root/root 223 2014-08-21 05:52 ./usr/bin/parallel-fastq
-rwxr-xr-x root/root 11021 2014-08-21 05:52 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4696 2014-08-21 05:52 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 15330 2014-08-21 05:52 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 22534 2014-08-21 05:52 ./usr/bin/maf-convert
-rwxr-xr-x root/root 4266 2014-08-21 05:52 ./usr/bin/maf-cull
-rwxr-xr-x root/root 8992 2014-08-21 05:52 ./usr/bin/maf-join
-rwxr-xr-x root/root 4762 2014-08-21 05:52 ./usr/bin/maf-swap
-rwxr-xr-x root/root 2027 2014-08-21 05:52 ./usr/bin/maf-sort
-rwxr-xr-x root/root 235388 2014-08-21 05:53 ./usr/bin/lastal
-rwxr-xr-x root/root 96020 2014-08-21 05:53 ./usr/bin/lastdb
-rwxr-xr-x root/root 263848 2014-08-21 05:53 ./usr/bin/lastex
-rwxr-xr-x root/root 116788 2014-08-21 05:53 ./usr/bin/last-split
-rwxr-xr-x root/root 5600 2014-08-21 05:53 ./usr/bin/last-merge-batches
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/share/
drwxr-xr-x root/root 0 2014-08-21 05:52 ./usr/share/man/
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/share/man/man1/
-rw-r--r-- root/root 536 2014-08-21 05:53 ./usr/share/man/man1/last-dotplot.1.gz
-rw-r--r-- root/root 1299 2014-08-21 05:53 ./usr/share/man/man1/lastal.1.gz
-rw-r--r-- root/root 689 2014-08-21 05:53 ./usr/share/man/man1/lastdb.1.gz
-rw-r--r-- root/root 614 2014-08-21 05:53 ./usr/share/man/man1/lastex.1.gz
-rw-r--r-- root/root 312 2014-08-21 05:53 ./usr/share/man/man1/maf-sort.1.gz
-rw-r--r-- root/root 337 2014-08-21 05:53 ./usr/share/man/man1/maf-swap.1.gz
-rw-r--r-- root/root 489 2014-08-21 05:53 ./usr/share/man/man1/last-map-probs.1.gz
-rw-r--r-- root/root 693 2014-08-21 05:53 ./usr/share/man/man1/last-split.1.gz
-rw-r--r-- root/root 279 2014-08-21 05:53 ./usr/share/man/man1/maf-join.1.gz
-rw-r--r-- root/root 564 2014-08-21 05:53 ./usr/share/man/man1/maf-convert.1.gz
-rw-r--r-- root/root 365 2014-08-21 05:53 ./usr/share/man/man1/maf-cull.1.gz
-rw-r--r-- root/root 645 2014-08-21 05:53 ./usr/share/man/man1/last-pair-probs.1.gz
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/share/doc/last-align/
-rw-r--r-- root/root 9815 2014-08-06 07:21 ./usr/share/doc/last-align/bisulfite.html
-rw-r--r-- root/root 2585 2014-08-06 07:21 ./usr/share/doc/last-align/bisulfite.txt
-rw-r--r-- root/root 11853 2014-08-06 07:21 ./usr/share/doc/last-align/FAQ.html
-rw-r--r-- root/root 2918 2014-08-06 07:21 ./usr/share/doc/last-align/FAQ.txt
-rw-r--r-- root/root 80 2014-08-06 07:21 ./usr/share/doc/last-align/last-doc.css
-rw-r--r-- root/root 10556 2014-08-06 07:21 ./usr/share/doc/last-align/last-map-probs.html
-rw-r--r-- root/root 2689 2014-08-06 07:21 ./usr/share/doc/last-align/last-map-probs.txt
-rw-r--r-- root/root 15072 2014-08-06 07:21 ./usr/share/doc/last-align/last-pair-probs.html
-rw-r--r-- root/root 2611 2014-08-06 07:21 ./usr/share/doc/last-align/last-scripts.txt
-rw-r--r-- root/root 20663 2014-08-06 07:21 ./usr/share/doc/last-align/last-split.html
-rw-r--r-- root/root 23416 2014-08-06 07:21 ./usr/share/doc/last-align/last-tutorial.html
-rw-r--r-- root/root 11810 2014-08-06 07:21 ./usr/share/doc/last-align/last.html
-rw-r--r-- root/root 11992 2014-08-06 07:21 ./usr/share/doc/last-align/maf-convert.html
-rw-r--r-- root/root 3578 2014-08-06 07:21 ./usr/share/doc/last-align/maf-convert.txt
-rw-r--r-- root/root 8293 2014-08-06 07:21 ./usr/share/doc/last-align/maf-cull.html
-rw-r--r-- root/root 1024 2014-08-06 07:21 ./usr/share/doc/last-align/maf-cull.txt
-rw-r--r-- root/root 624 2014-08-06 07:21 ./usr/share/doc/last-align/Makefile
-rw-r--r-- root/root 2736 2014-08-16 05:57 ./usr/share/doc/last-align/copyright
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/share/doc/last-align/examples/
-rw-r--r-- root/root 749 2014-08-06 07:21 ./usr/share/doc/last-align/examples/hoxd70.mat
-rwxr-xr-x root/root 1512 2014-08-06 07:21 ./usr/share/doc/last-align/examples/last-bisulfite-paired.sh
-rwxr-xr-x root/root 905 2014-08-06 07:21 ./usr/share/doc/last-align/examples/last-bisulfite.sh
-rwxr-xr-x root/root 979 2014-08-06 07:21 ./usr/share/doc/last-align/examples/multiMito.sh
-rw-r--r-- root/root 712 2014-08-06 07:21 ./usr/share/doc/last-align/examples/titv212.mat
-rw-r--r-- root/root 539 2014-08-06 07:21 ./usr/share/doc/last-align/examples/vertebrateMito.gc
-rw-r--r-- root/root 919 2014-08-06 07:21 ./usr/share/doc/last-align/examples/yass.seed
-rw-r--r-- root/root 5504 2014-08-06 07:21 ./usr/share/doc/last-align/examples/chickenMito.fa.gz
-rw-r--r-- root/root 5675 2014-08-06 07:21 ./usr/share/doc/last-align/examples/fuguMito.fa.gz
-rw-r--r-- root/root 5562 2014-08-06 07:21 ./usr/share/doc/last-align/examples/humanMito.fa.gz
-rw-r--r-- root/root 5424 2014-08-06 07:21 ./usr/share/doc/last-align/examples/mouseMito.fa.gz
-rw-r--r-- root/root 50644 2014-08-06 07:21 ./usr/share/doc/last-align/examples/multiMito.maf.gz
-rw-r--r-- root/root 9148 2014-08-06 07:21 ./usr/share/doc/last-align/examples/myalns.maf.gz
-rw-r--r-- root/root 2431 2014-08-06 07:21 ./usr/share/doc/last-align/last-pair-probs.txt.gz
-rw-r--r-- root/root 3347 2014-08-06 07:21 ./usr/share/doc/last-align/last-split.txt.gz
-rw-r--r-- root/root 4572 2014-08-06 07:21 ./usr/share/doc/last-align/last-tutorial.txt.gz
-rw-r--r-- root/root 2082 2014-08-06 07:21 ./usr/share/doc/last-align/last.txt.gz
-rw-r--r-- root/root 5895 2014-08-06 07:21 ./usr/share/doc/last-align/lastal.txt.gz
-rw-r--r-- root/root 2474 2014-08-06 07:21 ./usr/share/doc/last-align/lastdb.txt.gz
-rw-r--r-- root/root 2628 2014-08-06 07:21 ./usr/share/doc/last-align/lastex.txt.gz
-rw-r--r-- root/root 2347 2014-08-06 07:21 ./usr/share/doc/last-align/tag-seeds.txt.gz
-rw-r--r-- root/root 3701 2014-08-16 06:20 ./usr/share/doc/last-align/changelog.Debian.gz
-rw-r--r-- root/root 201 2010-05-23 14:43 ./usr/share/doc/last-align/NEWS.Debian.gz
-rw-r--r-- root/root 20451 2014-08-06 07:21 ./usr/share/doc/last-align/changelog.gz
drwxr-xr-x root/root 0 2014-08-21 05:53 ./usr/share/doc-base/
-rw-r--r-- root/root 291 2014-01-28 17:32 ./usr/share/doc-base/last-align-scripts
-rw-r--r-- root/root 281 2011-03-11 22:51 ./usr/share/doc-base/last-align-manual
-rw-r--r-- root/root 486 2010-06-24 10:06 ./usr/share/doc-base/last-align-lastex
-rw-r--r-- root/root 294 2008-12-28 12:36 ./usr/share/doc-base/last-align-seeds
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 25168
Build-Time: 477
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 230
Job: last-align_475-1
Machine Architecture: armhf
Package: last-align
Package-Time: 756
Source-Version: 475-1
Space: 25168
Status: successful
Version: 475-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140821-0553
Build needed 00:12:36, 25168k disc space