last-align →
490-1 →
armhf → 2014-11-03 07:53:41
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testwandboard
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║ last-align 490-1 (armhf) 03 Nov 2014 07:39 ║
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Package: last-align
Version: 490-1
Source Version: 490-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/last-align-hm32w2/last-align-490' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/last-align-hm32w2' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-de29e05c-54dc-43b9-8ccd-62ef2f4c5ef0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7716 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8926 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
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└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Building dependency tree...
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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 287 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main last-align 490-1 (dsc) [1992 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main last-align 490-1 (tar) [278 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main last-align 490-1 (diff) [7620 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-XlAQKW/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
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 51 not upgraded.
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, python-imaging
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, python-imaging
dpkg-deb: building package `sbuild-build-depends-last-align-dummy' in `/«BUILDDIR»/resolver-E89Pgl/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 dpkg-dev file gettext gettext-base groff-base
help2man intltool-debian libasprintf0c2 libcroco3 libdpkg-perl libexpat1
libffi6 libfreetype6 libglib2.0-0 libjbig0 libjpeg8 liblcms2-2
liblocale-gettext-perl libmagic1 libpipeline1 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 debian-keyring 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:
libalgorithm-merge-perl curl wget lynx-cur autopoint libasprintf-dev
libgettextpo-dev libfile-fcntllock-perl libglib2.0-data shared-mime-info
xdg-user-dirs 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 liblocale-gettext-perl libmagic1
libpipeline1 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
The following packages will be upgraded:
dpkg-dev libdpkg-perl
2 upgraded, 41 newly installed, 0 to remove and 49 not upgraded.
Need to get 17.5 MB/17.5 MB of archives.
After this operation, 46.2 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.1-1 [21.8 kB]
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Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.6 [177 kB]
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Get:6 http://172.17.0.1/private/ jessie-staging/main liblocale-gettext-perl armhf 1.05-8+b1 [18.4 kB]
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Get:15 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.2-2 [403 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
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Get:20 http://172.17.0.1/private/ jessie-staging/main liblcms2-2 armhf 2.6-3 [113 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libtiff5 armhf 4.0.3-10 [191 kB]
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 0.4.1-1.2 [164 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libwebpdemux1 armhf 0.4.1-1.2 [49.4 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libwebpmux1 armhf 0.4.1-1.2 [54.6 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.19-2 [57.8 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.19.2-3 [116 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.57 [35.8 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.8-11 [1805 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.8-11 [249 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 dpkg-dev all 1.17.21 [1502 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libdpkg-perl all 1.17.21 [1038 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.19.2-3 [1164 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20141022 [812 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.46.4 [139 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main python-pil armhf 2.5.1-1 [299 kB]
Get:42 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_2.24.51.20140918-1 dpkg-dev_1.17.21 g++-4.6_4.6.4-5+rpi1 g++-4.9_4.9.1-15 gcc-4.6_4.6.4-5+rpi1 gcc-4.8_4.8.3-11 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 libstdc++6-4.6-dev_4.6.4-5+rpi1 linux-libc-dev_3.14.4-1+rpi1+b4
Package versions: apt_1.0.9.1 base-files_7.5+rpi1 base-passwd_3.5.36 bash_4.3-9.2 binutils_2.24.51.20140918-1 bsdmainutils_9.0.6 bsdutils_1:2.20.1-5.9 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpio_2.11+dfsg-2 cpp_4:4.9.1-1 cpp-4.6_4.6.4-5+rpi1 cpp-4.8_4.8.3-11 cpp-4.9_4.9.1-15 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20141022 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.21 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4.4.2-9 g++_4:4.9.1-1 g++-4.6_4.6.4-5+rpi1 g++-4.9_4.9.1-15 gcc_4:4.9.1-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-5+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-11 gcc-4.8-base_4.8.3-11 gcc-4.9_4.9.1-15 gcc-4.9-base_4.9.1-15 gettext_0.19.2-3 gettext-base_0.19.2-3 gnupg_1.4.18-4 gpgv_1.4.18-4 grep_2.20-3 groff-base_1.22.2-8 gzip_1.6-3 help2man_1.46.4 hostname_3.15 init_1.21 initramfs-tools_0.116 initscripts_2.88dsf-53.4 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.1 libarchive-extract-perl_0.72-1 libasan0_4.8.3-11 libasan1_4.9.1-15 libasprintf0c2_0.19.2-3 libatomic1_4.9.1-15 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.20.1-5.9 libbz2-1.0_1.0.6-7 libc-bin_2.19-11 libc-dev-bin_2.19-11 libc6_2.19-11 libc6-dev_2.19-11 libcap2_1:2.24-6 libcgi-pm-perl_4.03-1 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1 libcroco3_0.6.8-3 libdb5.1_5.1.29-6 libdb5.3_5.3.28-6 libdbus-1-3_1.8.6-2 libdebconfclient0_0.192 libdpkg-perl_1.17.21 libdrm2_2.4.56-1 libexpat1_2.1.0-6 libfakeroot_1.20.1-1.1 libffi6_3.1-2 libfreetype6_2.5.2-2 libgc1c2_1:7.2d-6.3 libgcc-4.8-dev_4.8.3-11 libgcc-4.9-dev_4.9.1-15 libgcc1_1:4.9.1-15 libgdbm3_1.8.3-13 libglib2.0-0_2.42.0-2 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.1-15 libisl10_0.12.2-2 libjbig0_2.1-3.1 libjpeg8_8d1-2 libklibc_2.0.3-1+rpi1 libkmod2_18-3 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-2 libmodule-pluggable-perl_5.1-1 libmount1_2.20.1-5.9 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libpackage-constants-perl_0.04-1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_1:8.35-3 libpipeline1_1.3.1-1 libpng12-0_1.2.50-2 libpod-latex-perl_0.61-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-7 libpython-stdlib_2.7.8-1 libpython2.7-minimal_2.7.8-11 libpython2.7-stdlib_2.7.8-11 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-1 libsqlite3-0_3.8.7-1 libss2_1.42.12-1 libssl1.0.0_1.0.1j-1 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 libstdc++6-4.6-dev_4.6.4-5+rpi1 libswitch-perl_2.17-2 libtiff5_4.0.3-10 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.1-15 libudev0_175-7.2 libudev1_208-8 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.9 libwebp5_0.4.1-1.2 libwebpdemux1_0.4.1-1.2 libwebpmux1_0.4.1-1.2 libxml2_2.9.1+dfsg1-4 linux-libc-dev_3.14.4-1+rpi1+b4 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.7.0.2-2 mawk_1.3.3-17 mime-support_3.57 mount_2.20.1-5.9 multiarch-support_2.19-11 nano_2.2.6-3 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-2 patch_2.7.1-6 perl_5.20.1-1 perl-base_5.20.1-1 perl-modules_5.20.1-1 plymouth_0.9.0-7 po-debconf_1.0.16+nmu3 procps_1:3.3.9-7 python_2.7.8-1 python-imaging_2.5.1-1 python-minimal_2.7.8-1 python-pil_2.5.1-1 python2.7_2.7.8-11 python2.7-minimal_2.7.8-11 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 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-53.4 sysvinit_2.88dsf-53.4 sysvinit-core_2.88dsf-53.4 sysvinit-utils_2.88dsf-53.4 tar_1.27.1-2 tzdata_2014g-1 udev_208-8 util-linux_2.20.1-5.9 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 Thu Oct 23 20:52:57 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./last-align_490-1.dsc
dpkg-source: info: extracting last-align in last-align-490
dpkg-source: info: unpacking last-align_490.orig.tar.xz
dpkg-source: info: unpacking last-align_490-1.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-de29e05c-54dc-43b9-8ccd-62ef2f4c5ef0
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 490-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build last-align-490
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-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic" CFLAGS="-g -O2 -fstack-protector-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -Wformat -Werror=format-security -c -o CA_code/lambda_calculator.o CA_code/lambda_calculator.c
g++ -g -O2 -fstack-protector-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c
gcc -g -O2 -fstack-protector-strong -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»'
mkdir -p /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1/
help2man --no-info --version-string="490" \
--name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
/«PKGBUILDDIR»/scripts/last-dotplot > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-dotplot.1
help2man --no-info --version-string="490" \
--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="490" \
--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="490" \
--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="490" \
--name="Sort MAF-format alignments by sequence name" \
/«PKGBUILDDIR»/scripts/maf-sort > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-sort.1
help2man --no-info --version-string="490" \
--name="changes the order of the sequences in MAF-format alignments" \
/«PKGBUILDDIR»/scripts/maf-swap > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-swap.1
help2man --no-info --version-string="490" \
--name="Add extra column with mapping probabilities" \
/«PKGBUILDDIR»/scripts/last-map-probs > /«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="490" \
# --name="Read files of lastal output, merge corresponding batches, and write them." \
# /«PKGBUILDDIR»/scripts/last-merge-batches > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-merge-batches.1
#help2man --no-info --version-string="490" \
# --name="Clean up MAF-format alignments" \
# /«PKGBUILDDIR»/scripts/last-reduce-alignments > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-reduce-alignments.1
#help2man --no-info --version-string="490" \
# --name='Remove MAF-format alignments which are "dominated" by others' \
# /«PKGBUILDDIR»/scripts/last-remove-dominated > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//last-remove-dominated.1
help2man --no-info --version-string="490" \
--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="490" \
--name="Join two or more sets of MAF-format multiple alignments" \
/«PKGBUILDDIR»/scripts/maf-join > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-join.1
help2man --no-info --version-string="490" \
--name="Convert MAF-format alignments to tabular format" \
/«PKGBUILDDIR»/scripts/maf-convert > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-convert.1
help2man --no-info --version-string="490" \
--name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \
/«PKGBUILDDIR»/scripts/maf-cull > /«PKGBUILDDIR»/debian/last-align/usr/share/man/man1//maf-cull.1
help2man --no-info --version-string="490" \
--name="Read alignments of paired DNA reads to a genome" \
/«PKGBUILDDIR»/scripts/last-pair-probs > /«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/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/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/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_490-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../last-align_490-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build last-align-490
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20141103-0753
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_490-1_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Thu, 23 Oct 2014 22:30:48 +0200
Source: last-align
Binary: last-align
Architecture: armhf
Version: 490-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (490-1) unstable; urgency=medium
.
* New upstream version
* get-orig-source target now with xz compression
* cme fix dpkg-control
* Upstream dropped .py suffix - adpapt help2man calls in d/rules
Checksums-Sha1:
fa65bc198a5059592b06c892c2f83b1728e63209 407964 last-align_490-1_armhf.deb
Checksums-Sha256:
472ae57fb447cce05ff63b60ac4e51fd8a97402e746b335464038f622ae9d2e7 407964 last-align_490-1_armhf.deb
Files:
a936c884e248b7763e9a7cf6c5f2fe09 407964 science optional last-align_490-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
last-align_490-1_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 407964 bytes: control archive=3172 bytes.
1176 bytes, 25 lines control
5357 bytes, 76 lines md5sums
Package: last-align
Version: 490-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1086
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 2014-11-03 07:52 ./
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/bin/
-rwxr-xr-x root/root 11475 2014-11-03 07:52 ./usr/bin/last-dotplot
-rwxr-xr-x root/root 4696 2014-11-03 07:52 ./usr/bin/last-map-probs
-rwxr-xr-x root/root 15330 2014-11-03 07:52 ./usr/bin/last-pair-probs
-rwxr-xr-x root/root 3931 2014-11-03 07:52 ./usr/bin/last-postmask
-rwxr-xr-x root/root 23800 2014-11-03 07:52 ./usr/bin/maf-convert
-rwxr-xr-x root/root 4266 2014-11-03 07:52 ./usr/bin/maf-cull
-rwxr-xr-x root/root 8992 2014-11-03 07:52 ./usr/bin/maf-join
-rwxr-xr-x root/root 2027 2014-11-03 07:52 ./usr/bin/maf-sort
-rwxr-xr-x root/root 4762 2014-11-03 07:52 ./usr/bin/maf-swap
-rwxr-xr-x root/root 234 2014-11-03 07:52 ./usr/bin/parallel-fasta
-rwxr-xr-x root/root 223 2014-11-03 07:52 ./usr/bin/parallel-fastq
-rwxr-xr-x root/root 239480 2014-11-03 07:52 ./usr/bin/lastal
-rwxr-xr-x root/root 100116 2014-11-03 07:52 ./usr/bin/lastdb
-rwxr-xr-x root/root 267944 2014-11-03 07:52 ./usr/bin/lastex
-rwxr-xr-x root/root 116788 2014-11-03 07:52 ./usr/bin/last-split
-rwxr-xr-x root/root 5600 2014-11-03 07:52 ./usr/bin/last-merge-batches
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/man/
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/man/man1/
-rw-r--r-- root/root 533 2014-11-03 07:52 ./usr/share/man/man1/last-dotplot.1.gz
-rw-r--r-- root/root 1313 2014-11-03 07:52 ./usr/share/man/man1/lastal.1.gz
-rw-r--r-- root/root 690 2014-11-03 07:52 ./usr/share/man/man1/lastdb.1.gz
-rw-r--r-- root/root 613 2014-11-03 07:52 ./usr/share/man/man1/lastex.1.gz
-rw-r--r-- root/root 309 2014-11-03 07:52 ./usr/share/man/man1/maf-sort.1.gz
-rw-r--r-- root/root 332 2014-11-03 07:52 ./usr/share/man/man1/maf-swap.1.gz
-rw-r--r-- root/root 484 2014-11-03 07:52 ./usr/share/man/man1/last-map-probs.1.gz
-rw-r--r-- root/root 694 2014-11-03 07:52 ./usr/share/man/man1/last-split.1.gz
-rw-r--r-- root/root 278 2014-11-03 07:52 ./usr/share/man/man1/maf-join.1.gz
-rw-r--r-- root/root 558 2014-11-03 07:52 ./usr/share/man/man1/maf-convert.1.gz
-rw-r--r-- root/root 365 2014-11-03 07:52 ./usr/share/man/man1/maf-cull.1.gz
-rw-r--r-- root/root 640 2014-11-03 07:52 ./usr/share/man/man1/last-pair-probs.1.gz
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/doc/last-align/
-rw-r--r-- root/root 9913 2014-10-07 18:04 ./usr/share/doc/last-align/bisulfite.html
-rw-r--r-- root/root 2585 2014-10-07 18:04 ./usr/share/doc/last-align/bisulfite.txt
-rw-r--r-- root/root 11951 2014-10-07 18:04 ./usr/share/doc/last-align/FAQ.html
-rw-r--r-- root/root 2918 2014-10-07 18:04 ./usr/share/doc/last-align/FAQ.txt
-rw-r--r-- root/root 178 2014-10-07 18:04 ./usr/share/doc/last-align/last-doc.css
-rw-r--r-- root/root 10648 2014-10-07 18:04 ./usr/share/doc/last-align/last-map-probs.html
-rw-r--r-- root/root 2683 2014-10-07 18:04 ./usr/share/doc/last-align/last-map-probs.txt
-rw-r--r-- root/root 15158 2014-10-07 18:04 ./usr/share/doc/last-align/last-pair-probs.html
-rw-r--r-- root/root 7969 2014-10-07 18:04 ./usr/share/doc/last-align/last-postmask.html
-rw-r--r-- root/root 998 2014-10-07 18:04 ./usr/share/doc/last-align/last-postmask.txt
-rw-r--r-- root/root 2551 2014-10-07 18:04 ./usr/share/doc/last-align/last-scripts.txt
-rw-r--r-- root/root 20761 2014-10-07 18:04 ./usr/share/doc/last-align/last-split.html
-rw-r--r-- root/root 23514 2014-10-07 18:04 ./usr/share/doc/last-align/last-tutorial.html
-rw-r--r-- root/root 11908 2014-10-07 18:04 ./usr/share/doc/last-align/last.html
-rw-r--r-- root/root 12081 2014-10-07 18:04 ./usr/share/doc/last-align/maf-convert.html
-rw-r--r-- root/root 3569 2014-10-07 18:04 ./usr/share/doc/last-align/maf-convert.txt
-rw-r--r-- root/root 8385 2014-10-07 18:04 ./usr/share/doc/last-align/maf-cull.html
-rw-r--r-- root/root 1018 2014-10-07 18:04 ./usr/share/doc/last-align/maf-cull.txt
-rw-r--r-- root/root 643 2014-10-07 18:04 ./usr/share/doc/last-align/Makefile
-rw-r--r-- root/root 2748 2014-10-23 20:46 ./usr/share/doc/last-align/copyright
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/doc/last-align/examples/
-rw-r--r-- root/root 749 2014-10-07 18:04 ./usr/share/doc/last-align/examples/hoxd70.mat
-rwxr-xr-x root/root 1509 2014-10-07 18:04 ./usr/share/doc/last-align/examples/last-bisulfite-paired.sh
-rwxr-xr-x root/root 905 2014-10-07 18:04 ./usr/share/doc/last-align/examples/last-bisulfite.sh
-rwxr-xr-x root/root 964 2014-10-07 18:04 ./usr/share/doc/last-align/examples/multiMito.sh
-rw-r--r-- root/root 712 2014-10-07 18:04 ./usr/share/doc/last-align/examples/titv212.mat
-rw-r--r-- root/root 539 2014-10-07 18:04 ./usr/share/doc/last-align/examples/vertebrateMito.gc
-rw-r--r-- root/root 919 2014-10-07 18:04 ./usr/share/doc/last-align/examples/yass.seed
-rw-r--r-- root/root 5504 2014-10-07 18:04 ./usr/share/doc/last-align/examples/chickenMito.fa.gz
-rw-r--r-- root/root 5675 2014-10-07 18:04 ./usr/share/doc/last-align/examples/fuguMito.fa.gz
-rw-r--r-- root/root 5562 2014-10-07 18:04 ./usr/share/doc/last-align/examples/humanMito.fa.gz
-rw-r--r-- root/root 5424 2014-10-07 18:04 ./usr/share/doc/last-align/examples/mouseMito.fa.gz
-rw-r--r-- root/root 50644 2014-10-07 18:04 ./usr/share/doc/last-align/examples/multiMito.maf.gz
-rw-r--r-- root/root 9148 2014-10-07 18:04 ./usr/share/doc/last-align/examples/myalns.maf.gz
-rw-r--r-- root/root 2427 2014-10-07 18:04 ./usr/share/doc/last-align/last-pair-probs.txt.gz
-rw-r--r-- root/root 3347 2014-10-07 18:04 ./usr/share/doc/last-align/last-split.txt.gz
-rw-r--r-- root/root 4572 2014-10-07 18:04 ./usr/share/doc/last-align/last-tutorial.txt.gz
-rw-r--r-- root/root 2082 2014-10-07 18:04 ./usr/share/doc/last-align/last.txt.gz
-rw-r--r-- root/root 5953 2014-10-07 18:04 ./usr/share/doc/last-align/lastal.txt.gz
-rw-r--r-- root/root 2565 2014-10-07 18:04 ./usr/share/doc/last-align/lastdb.txt.gz
-rw-r--r-- root/root 2628 2014-10-07 18:04 ./usr/share/doc/last-align/lastex.txt.gz
-rw-r--r-- root/root 2347 2014-10-07 18:04 ./usr/share/doc/last-align/tag-seeds.txt.gz
-rw-r--r-- root/root 3763 2014-10-23 20:40 ./usr/share/doc/last-align/changelog.Debian.gz
-rw-r--r-- root/root 201 2013-09-12 08:58 ./usr/share/doc/last-align/NEWS.Debian.gz
-rw-r--r-- root/root 20938 2014-10-07 18:04 ./usr/share/doc/last-align/changelog.gz
drwxr-xr-x root/root 0 2014-11-03 07:52 ./usr/share/doc-base/
-rw-r--r-- root/root 291 2014-01-28 17:31 ./usr/share/doc-base/last-align-scripts
-rw-r--r-- root/root 294 2013-09-12 08:58 ./usr/share/doc-base/last-align-seeds
-rw-r--r-- root/root 281 2013-09-12 08:58 ./usr/share/doc-base/last-align-manual
-rw-r--r-- root/root 486 2013-09-12 08:58 ./usr/share/doc-base/last-align-lastex
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 25368
Build-Time: 498
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 242
Job: last-align_490-1
Machine Architecture: armhf
Package: last-align
Package-Time: 793
Source-Version: 490-1
Space: 25368
Status: successful
Version: 490-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20141103-0753
Build needed 00:13:13, 25368k disc space