sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ fastx-toolkit 0.0.13.2-1 (armhf) 27 May 2012 19:43 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: fastx-toolkit Version: 0.0.13.2-1 Source Version: 0.0.13.2-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/fastx-toolkit-09B4hj/fastx-toolkit-0.0.13.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/fastx-toolkit-09B4hj' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-67ff277a-ebdc-411b-9e40-8e186f5a5ca7' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://repo.raspbian.lan testing InRelease [3588 B] Get:2 http://repo.raspbian.lan testing/main Sources [5963 kB] Get:3 http://repo.raspbian.lan testing/main armhf Packages [6684 kB] Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Fetched 12.7 MB in 28s (449 kB/s) Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'fastx-toolkit' packaging is maintained in the 'Git' version control system at: git://git.debian.org/debian-med/fastx-toolkit.git Need to get 564 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main fastx-toolkit 0.0.13.2-1 (dsc) [2148 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main fastx-toolkit 0.0.13.2-1 (tar) [545 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main fastx-toolkit 0.0.13.2-1 (diff) [16.9 kB] Fetched 564 kB in 0s (5126 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-Dqcf52/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 18 not upgraded. Need to get 0 B/706 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10669 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, pkg-config, libgtextutils-dev, help2man, libgd-graph-perl, libperlio-gzip-perl Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, pkg-config, libgtextutils-dev, help2man, libgd-graph-perl, libperlio-gzip-perl dpkg-deb: building package `sbuild-build-depends-fastx-toolkit-dummy' in `/«BUILDDIR»/resolver-v9WSDR/apt_archive/sbuild-build-depends-fastx-toolkit-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install fastx-toolkit build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils debhelper file fontconfig-config gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libexpat1 libffi5 libfontconfig1 libfreetype6 libgd-gd2-perl libgd-graph-perl libgd-text-perl libgd2-xpm libglib2.0-0 libgtextutils-dev libgtextutils0 libjpeg8 libmagic1 libpcre3 libperlio-gzip-perl libpipeline1 libpng12-0 libpopt0 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 libxpm4 man-db pkg-config po-debconf ttf-dejavu-core Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff ttf-dustin libgd-tools less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper file fontconfig-config gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libexpat1 libffi5 libfontconfig1 libfreetype6 libgd-gd2-perl libgd-graph-perl libgd-text-perl libgd2-xpm libglib2.0-0 libgtextutils-dev libgtextutils0 libjpeg8 libmagic1 libpcre3 libperlio-gzip-perl libpipeline1 libpng12-0 libpopt0 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 libxpm4 man-db pkg-config po-debconf sbuild-build-depends-fastx-toolkit-dummy ttf-dejavu-core 0 upgraded, 43 newly installed, 0 to remove and 18 not upgraded. Need to get 722 kB/14.6 MB of archives. After this operation, 36.5 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main libgd2-xpm armhf 2.0.36~rc1~dfsg-6.1 [222 kB] Get:2 http://repo.raspbian.lan/raspbian/ testing/main libgtextutils0 armhf 0.6.2-1 [21.0 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main libgtextutils-dev armhf 0.6.2-1 [26.0 kB] Get:4 http://repo.raspbian.lan/raspbian/ testing/main libperlio-gzip-perl armhf 0.18-1 [17.9 kB] Get:5 http://repo.raspbian.lan/raspbian/ testing/main libgd-text-perl all 0.86-8 [42.4 kB] Get:6 http://repo.raspbian.lan/raspbian/ testing/main libgd-graph-perl all 1.44-6 [393 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 722 kB in 0s (5197 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10669 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libpopt0:armhf. Unpacking libpopt0:armhf (from .../libpopt0_1.16-4_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9.1_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.3-1_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libexpat1:armhf. 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Selecting previously unselected package libgd-gd2-perl. Unpacking libgd-gd2-perl (from .../libgd-gd2-perl_1%3a2.46-3_armhf.deb) ... Selecting previously unselected package libgd-text-perl. Unpacking libgd-text-perl (from .../libgd-text-perl_0.86-8_all.deb) ... Selecting previously unselected package libgd-graph-perl. Unpacking libgd-graph-perl (from .../libgd-graph-perl_1.44-6_all.deb) ... Selecting previously unselected package sbuild-build-depends-fastx-toolkit-dummy. Unpacking sbuild-build-depends-fastx-toolkit-dummy (from .../sbuild-build-depends-fastx-toolkit-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libpopt0:armhf (1.16-4) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9.1) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.9.0-5) ... Setting up libfontconfig1:armhf (2.9.0-5) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.99.901-2) ... Setting up libx11-6:armhf (2:1.4.99.901-2) ... Setting up libxpm4:armhf (1:3.5.10-1) ... Setting up libgd2-xpm:armhf (2.0.36~rc1~dfsg-6.1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up autotools-dev (20120210.1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up help2man (1.40.9) ... Setting up libgtextutils0 (0.6.2-1) ... Setting up libgtextutils-dev (0.6.2-1) ... Setting up libperlio-gzip-perl (0.18-1) ... Setting up pkg-config (0.26-1) ... Setting up libgd-gd2-perl (1:2.46-3) ... Setting up libgd-text-perl (0.86-8) ... Setting up libgd-graph-perl (1.44-6) ... Setting up sbuild-build-depends-fastx-toolkit-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-32 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 autotools-dev_20120210.1 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 fontconfig-config_2.9.0-5 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 help2man_1.40.9 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-7 libattr1_1:2.4.46-7 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfontconfig1_2.9.0-5 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgd-gd2-perl_1:2.46-3 libgd-graph-perl_1.44-6 libgd-text-perl_0.86-8 libgd2-xpm_2.0.36~rc1~dfsg-6.1 libgdbm3_1.8.3-10 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-1.1 libgomp1_4.7.0-1.1+rpi libgtextutils-dev_0.6.2-1 libgtextutils0_0.6.2-1 libjpeg8_8d-1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-7 libncursesw5_5.9-7 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libperlio-gzip-perl_0.18-1 libpipeline1_1.2.1-1 libpng12-0_1.2.49-1 libpopt0_1.16-4 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 libslang2_2.2.4-10 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libx11-6_2:1.4.99.901-2 libx11-data_2:1.4.99.901-2 libxau6_1:1.0.7-1 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxml2_2.7.8.dfsg-9.1 libxpm4_1:3.5.10-1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 pkg-config_0.26-1 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastx-toolkit-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 ttf-dejavu-core_2.33-2 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue May 15 12:09:25 2012 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./fastx-toolkit_0.0.13.2-1.dsc dpkg-source: info: extracting fastx-toolkit in fastx-toolkit-0.0.13.2 dpkg-source: info: unpacking fastx-toolkit_0.0.13.2.orig.tar.bz2 dpkg-source: info: unpacking fastx-toolkit_0.0.13.2-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-67ff277a-ebdc-411b-9e40-8e186f5a5ca7 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package fastx-toolkit dpkg-buildpackage: source version 0.0.13.2-1 dpkg-source --before-build fastx-toolkit-0.0.13.2 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean rm -f debian/fastx-toolkit.substvars rm -f debian/fastx-toolkit.*.debhelper rm -rf debian/fastx-toolkit/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} \; \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \) rm -f *-stamp debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 805306365 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking how to run the C++ preprocessor... g++ -E checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for long long int... yes checking for ISO C++ TR1 include files... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GTEXTUTILS... yes configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/libfastx/Makefile config.status: creating src/fastx_clipper/Makefile config.status: creating src/fastq_to_fasta/Makefile config.status: creating src/fastx_quality_stats/Makefile config.status: creating src/fastq_quality_converter/Makefile config.status: creating src/fastx_trimmer/Makefile config.status: creating src/fastq_quality_filter/Makefile config.status: creating src/fastq_quality_trimmer/Makefile config.status: creating src/fastx_artifacts_filter/Makefile config.status: creating src/fastx_reverse_complement/Makefile config.status: creating src/fastx_collapser/Makefile config.status: creating src/fastx_uncollapser/Makefile config.status: creating src/seqalign_test/Makefile config.status: creating src/fasta_formatter/Makefile config.status: creating src/fasta_nucleotide_changer/Makefile config.status: creating src/fastx_renamer/Makefile config.status: creating src/fastq_masker/Makefile config.status: creating galaxy/Makefile config.status: creating galaxy/tools/Makefile config.status: creating galaxy/tools/fastx_toolkit/Makefile config.status: creating galaxy/tools/cshl_custom_fastx_toolkit/Makefile config.status: creating galaxy/test-data/Makefile config.status: creating galaxy/static/Makefile config.status: creating galaxy/static/fastx_icons/Makefile config.status: creating galaxy/tool-data/Makefile config.status: creating scripts/Makefile config.status: creating build_scripts/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j1 make[1]: Entering directory `/«PKGBUILDDIR»' make all-recursive make[2]: Entering directory `/«PKGBUILDDIR»' Making all in m4 make[3]: Entering directory `/«PKGBUILDDIR»/m4' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/«PKGBUILDDIR»/m4' Making all in src make[3]: Entering directory `/«PKGBUILDDIR»/src' Making all in libfastx make[4]: Entering directory `/«PKGBUILDDIR»/src/libfastx' gcc -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c chomp.c gcc -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx.c gcc -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx_args.c g++ -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o sequence_alignment.o sequence_alignment.cpp rm -f libfastx.a ar cru libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o ranlib libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/libfastx' Making all in fastx_clipper make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_clipper' g++ -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o fastx_clipper.o fastx_clipper.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z,relro -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_clipper' Making all in fastx_trimmer make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_trimmer' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx_trimmer.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_trimmer' Making all in fastx_quality_stats make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_quality_stats' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx_quality_stats.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_quality_stats' Making all in fastq_quality_converter make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_converter' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastq_quality_converter.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_converter' Making all in fastq_to_fasta make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_to_fasta' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastq_to_fasta.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_to_fasta' Making all in fastq_quality_filter make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_filter' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastq_quality_filter.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_filter' Making all in fastq_quality_trimmer make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastq_quality_trimmer.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' Making all in fastx_artifacts_filter make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx_artifacts_filter.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastx_artifacts_filter fastx_artifacts_filter.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_artifacts_filter fastx_artifacts_filter.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' Making all in fastx_reverse_complement make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx_reverse_complement.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastx_reverse_complement fastx_reverse_complement.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_reverse_complement fastx_reverse_complement.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' Making all in fastx_collapser make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_collapser' g++ -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o fastx_collapser.o fastx_collapser.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z,relro -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_collapser' Making all in fastx_uncollapser make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_uncollapser' g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/gtextutils -I../libfastx -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o fastx_uncollapser.o fastx_uncollapser.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z,relro -o fastx_uncollapser fastx_uncollapser.o -lgtextutils ../libfastx/libfastx.a libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_uncollapser fastx_uncollapser.o -lgtextutils ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_uncollapser' Making all in seqalign_test make[4]: Entering directory `/«PKGBUILDDIR»/src/seqalign_test' g++ -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o seqalign_test.o seqalign_test.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z,relro -o seqalign_test seqalign_test.o ../libfastx/libfastx.a libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o seqalign_test seqalign_test.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/seqalign_test' Making all in fasta_formatter make[4]: Entering directory `/«PKGBUILDDIR»/src/fasta_formatter' g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/gtextutils -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o fasta_formatter.o fasta_formatter.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z,relro -o fasta_formatter fasta_formatter.o -lgtextutils ../libfastx/libfastx.a libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fasta_formatter fasta_formatter.o -lgtextutils ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fasta_formatter' Making all in fasta_nucleotide_changer make[4]: Entering directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fasta_nucleotide_changer.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fasta_nucleotide_changer fasta_nucleotide_changer.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fasta_nucleotide_changer fasta_nucleotide_changer.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' Making all in fastx_renamer make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_renamer' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastx_renamer.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_renamer' Making all in fastq_masker make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_masker' gcc -DHAVE_CONFIG_H -I. -I../.. -I../libfastx -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -c fastq_masker.c /bin/bash ../../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z,relro -o fastq_masker fastq_masker.o ../libfastx/libfastx.a libtool: link: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastq_masker fastq_masker.o ../libfastx/libfastx.a make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_masker' make[4]: Entering directory `/«PKGBUILDDIR»/src' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src' make[3]: Leaving directory `/«PKGBUILDDIR»/src' Making all in doc make[3]: Entering directory `/«PKGBUILDDIR»/doc' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/«PKGBUILDDIR»/doc' Making all in galaxy make[3]: Entering directory `/«PKGBUILDDIR»/galaxy' Making all in tools make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' Making all in fastx_toolkit make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' make[5]: Nothing to be done for `all'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' Making all in cshl_custom_fastx_toolkit make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[5]: Nothing to be done for `all'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' make[5]: Nothing to be done for `all-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' Making all in test-data make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/test-data' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/test-data' Making all in static make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/static' Making all in fastx_icons make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[5]: Nothing to be done for `all'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/static' make[5]: Nothing to be done for `all-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' Making all in tool-data make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tool-data' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tool-data' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy' Making all in scripts make[3]: Entering directory `/«PKGBUILDDIR»/scripts' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/«PKGBUILDDIR»/scripts' Making all in build_scripts make[3]: Entering directory `/«PKGBUILDDIR»/build_scripts' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/«PKGBUILDDIR»/build_scripts' make[3]: Entering directory `/«PKGBUILDDIR»' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a make -j1 check make[1]: Entering directory `/«PKGBUILDDIR»' Making check in m4 make[2]: Entering directory `/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/«PKGBUILDDIR»/m4' Making check in src make[2]: Entering directory `/«PKGBUILDDIR»/src' Making check in libfastx make[3]: Entering directory `/«PKGBUILDDIR»/src/libfastx' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/libfastx' Making check in fastx_clipper make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_clipper' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_clipper' Making check in fastx_trimmer make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_trimmer' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_trimmer' Making check in fastx_quality_stats make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_quality_stats' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_quality_stats' Making check in fastq_quality_converter make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_converter' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_converter' Making check in fastq_to_fasta make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_to_fasta' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_to_fasta' Making check in fastq_quality_filter make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_filter' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_filter' Making check in fastq_quality_trimmer make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' Making check in fastx_artifacts_filter make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' Making check in fastx_reverse_complement make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' Making check in fastx_collapser make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_collapser' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_collapser' Making check in fastx_uncollapser make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_uncollapser' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_uncollapser' Making check in seqalign_test make[3]: Entering directory `/«PKGBUILDDIR»/src/seqalign_test' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/seqalign_test' Making check in fasta_formatter make[3]: Entering directory `/«PKGBUILDDIR»/src/fasta_formatter' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fasta_formatter' Making check in fasta_nucleotide_changer make[3]: Entering directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' Making check in fastx_renamer make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_renamer' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_renamer' Making check in fastq_masker make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_masker' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_masker' make[3]: Entering directory `/«PKGBUILDDIR»/src' make[3]: Nothing to be done for `check-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' Making check in doc make[2]: Entering directory `/«PKGBUILDDIR»/doc' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/«PKGBUILDDIR»/doc' Making check in galaxy make[2]: Entering directory `/«PKGBUILDDIR»/galaxy' Making check in tools make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' Making check in fastx_toolkit make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' make[4]: Nothing to be done for `check'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' Making check in cshl_custom_fastx_toolkit make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[4]: Nothing to be done for `check'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' make[4]: Nothing to be done for `check-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' Making check in test-data make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/test-data' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/test-data' Making check in static make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/static' Making check in fastx_icons make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[4]: Nothing to be done for `check'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/static' make[4]: Nothing to be done for `check-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' Making check in tool-data make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/tool-data' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/tool-data' make[3]: Entering directory `/«PKGBUILDDIR»/galaxy' make[3]: Nothing to be done for `check-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy' make[2]: Leaving directory `/«PKGBUILDDIR»/galaxy' Making check in scripts make[2]: Entering directory `/«PKGBUILDDIR»/scripts' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/«PKGBUILDDIR»/scripts' Making check in build_scripts make[2]: Entering directory `/«PKGBUILDDIR»/build_scripts' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/«PKGBUILDDIR»/build_scripts' make[2]: Entering directory `/«PKGBUILDDIR»' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f debian/fastx-toolkit.substvars rm -f debian/fastx-toolkit.*.debhelper rm -rf debian/fastx-toolkit/ dh_installdirs -a install -d debian/fastx-toolkit dh_auto_install -a make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/fastx-toolkit AM_UPDATE_INFO_DIR=no make[1]: Entering directory `/«PKGBUILDDIR»' Making install in m4 make[2]: Entering directory `/«PKGBUILDDIR»/m4' make[3]: Entering directory `/«PKGBUILDDIR»/m4' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/share/aclocal" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/aclocal" /usr/bin/install -c -m 644 ax_c_long_long.m4 ax_cxx_header_stdcxx_tr1.m4 '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/aclocal' make[3]: Leaving directory `/«PKGBUILDDIR»/m4' make[2]: Leaving directory `/«PKGBUILDDIR»/m4' Making install in src make[2]: Entering directory `/«PKGBUILDDIR»/src' Making install in libfastx make[3]: Entering directory `/«PKGBUILDDIR»/src/libfastx' make[4]: Entering directory `/«PKGBUILDDIR»/src/libfastx' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/libfastx' make[3]: Leaving directory `/«PKGBUILDDIR»/src/libfastx' Making install in fastx_clipper make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_clipper' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_clipper' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_clipper '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_clipper /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_clipper make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_clipper' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_clipper' Making install in fastx_trimmer make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_trimmer' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_trimmer' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_trimmer '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_trimmer /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_trimmer make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_trimmer' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_trimmer' Making install in fastx_quality_stats make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_quality_stats' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_quality_stats' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_quality_stats '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_quality_stats /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_quality_stats make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_quality_stats' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_quality_stats' Making install in fastq_quality_converter make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_converter' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_converter' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastq_quality_converter '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastq_quality_converter /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_quality_converter make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_converter' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_converter' Making install in fastq_to_fasta make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_to_fasta' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_to_fasta' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastq_to_fasta '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastq_to_fasta /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_to_fasta make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_to_fasta' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_to_fasta' Making install in fastq_quality_filter make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_filter' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_filter' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastq_quality_filter '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastq_quality_filter /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_quality_filter make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_filter' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_filter' Making install in fastq_quality_trimmer make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastq_quality_trimmer '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastq_quality_trimmer /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_quality_trimmer make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_quality_trimmer' Making install in fastx_artifacts_filter make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_artifacts_filter '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_artifacts_filter /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_artifacts_filter make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_artifacts_filter' Making install in fastx_reverse_complement make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_reverse_complement '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_reverse_complement /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_reverse_complement make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_reverse_complement' Making install in fastx_collapser make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_collapser' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_collapser' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_collapser '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_collapser /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_collapser make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_collapser' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_collapser' Making install in fastx_uncollapser make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_uncollapser' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_uncollapser' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_uncollapser '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_uncollapser /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_uncollapser make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_uncollapser' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_uncollapser' Making install in seqalign_test make[3]: Entering directory `/«PKGBUILDDIR»/src/seqalign_test' make[4]: Entering directory `/«PKGBUILDDIR»/src/seqalign_test' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/seqalign_test' make[3]: Leaving directory `/«PKGBUILDDIR»/src/seqalign_test' Making install in fasta_formatter make[3]: Entering directory `/«PKGBUILDDIR»/src/fasta_formatter' make[4]: Entering directory `/«PKGBUILDDIR»/src/fasta_formatter' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fasta_formatter '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fasta_formatter /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fasta_formatter make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fasta_formatter' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fasta_formatter' Making install in fasta_nucleotide_changer make[3]: Entering directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' make[4]: Entering directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fasta_nucleotide_changer '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fasta_nucleotide_changer /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fasta_nucleotide_changer make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fasta_nucleotide_changer' Making install in fastx_renamer make[3]: Entering directory `/«PKGBUILDDIR»/src/fastx_renamer' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_renamer' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastx_renamer '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastx_renamer /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_renamer make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_renamer' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastx_renamer' Making install in fastq_masker make[3]: Entering directory `/«PKGBUILDDIR»/src/fastq_masker' make[4]: Entering directory `/«PKGBUILDDIR»/src/fastq_masker' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /bin/bash ../../libtool --mode=install /usr/bin/install -c fastq_masker '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' libtool: install: /usr/bin/install -c fastq_masker /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_masker make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastq_masker' make[3]: Leaving directory `/«PKGBUILDDIR»/src/fastq_masker' make[3]: Entering directory `/«PKGBUILDDIR»/src' make[4]: Entering directory `/«PKGBUILDDIR»/src' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src' make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' Making install in doc make[2]: Entering directory `/«PKGBUILDDIR»/doc' make[3]: Entering directory `/«PKGBUILDDIR»/doc' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/doc' make[2]: Leaving directory `/«PKGBUILDDIR»/doc' Making install in galaxy make[2]: Entering directory `/«PKGBUILDDIR»/galaxy' Making install in tools make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' Making install in fastx_toolkit make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/fastx_toolkit' Making install in cshl_custom_fastx_toolkit make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools/cshl_custom_fastx_toolkit' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/tools' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/tools' Making install in test-data make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/test-data' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/test-data' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/test-data' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/test-data' Making install in static make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/static' Making install in fastx_icons make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/static/fastx_icons' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/static' make[5]: Entering directory `/«PKGBUILDDIR»/galaxy/static' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/static' Making install in tool-data make[3]: Entering directory `/«PKGBUILDDIR»/galaxy/tool-data' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy/tool-data' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy/tool-data' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy/tool-data' make[3]: Entering directory `/«PKGBUILDDIR»/galaxy' make[4]: Entering directory `/«PKGBUILDDIR»/galaxy' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/galaxy' make[3]: Leaving directory `/«PKGBUILDDIR»/galaxy' make[2]: Leaving directory `/«PKGBUILDDIR»/galaxy' Making install in scripts make[2]: Entering directory `/«PKGBUILDDIR»/scripts' make[3]: Entering directory `/«PKGBUILDDIR»/scripts' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin" /usr/bin/install -c fastx_barcode_splitter.pl fastx_nucleotide_distribution_graph.sh fastx_nucleotide_distribution_line_graph.sh fastq_quality_boxplot_graph.sh fasta_clipping_histogram.pl '/«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/scripts' make[2]: Leaving directory `/«PKGBUILDDIR»/scripts' Making install in build_scripts make[2]: Entering directory `/«PKGBUILDDIR»/build_scripts' make[3]: Entering directory `/«PKGBUILDDIR»/build_scripts' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/build_scripts' make[2]: Leaving directory `/«PKGBUILDDIR»/build_scripts' make[2]: Entering directory `/«PKGBUILDDIR»' make[3]: Entering directory `/«PKGBUILDDIR»' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules override_dh_install make[1]: Entering directory `/«PKGBUILDDIR»' dh_install rm --recursive /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/aclocal make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installdocs -a install -g 0 -o 0 -d debian/fastx-toolkit/usr/share/doc/fastx-toolkit cp -a NEWS debian/fastx-toolkit/usr/share/doc/fastx-toolkit cp -a README debian/fastx-toolkit/usr/share/doc/fastx-toolkit cp -a THANKS debian/fastx-toolkit/usr/share/doc/fastx-toolkit chown -R 0:0 debian/fastx-toolkit/usr/share/doc chmod -R go=rX debian/fastx-toolkit/usr/share/doc chmod -R u\+rw debian/fastx-toolkit/usr/share/doc install -g 0 -o 0 -m 644 -p debian/README.Debian debian/fastx-toolkit/usr/share/doc/fastx-toolkit/README.Debian install -g 0 -o 0 -m 644 -p debian/copyright debian/fastx-toolkit/usr/share/doc/fastx-toolkit/copyright debian/rules override_dh_installchangelogs make[1]: Entering directory `/«PKGBUILDDIR»' dh_installchangelogs -k NEWS install -o 0 -g 0 -p -m644 debian/changelog debian/fastx-toolkit/usr/share/doc/fastx-toolkit/changelog.Debian install -o 0 -g 0 -p -m644 NEWS debian/fastx-toolkit/usr/share/doc/fastx-toolkit/changelog ln -sf changelog debian/fastx-toolkit/usr/share/doc/fastx-toolkit/NEWS make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory `/«PKGBUILDDIR»' mkdir -p /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1 # The name strings are obtained from # http://hannonlab.cshl.edu/fastx_toolkit/ (Section "Available Tools") # and # http://hannonlab.cshl.edu/fastx_toolkit/commandline.html help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='changes the width of sequences line in a FASTA file' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fasta_formatter > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fasta_formatter.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='Convets FASTA sequences from/to RNA/DNA' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fasta_nucleotide_changer > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fasta_nucleotide_changer.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name="Masks nucleotides with 'N' (or other character) based on quality" \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_masker > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastq_masker.1 # FIXME: The tool `fasta_quality_converter` was NOT described at the URLs above help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='Converts sequences based on quality' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_quality_converter > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastq_quality_converter.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='Filters sequences based on quality' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_quality_filter > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastq_quality_filter.1 dh_installman debian/fastq_quality_trimmer.1 install -p -m644 debian/fastq_quality_trimmer.1 debian/fastx-toolkit/usr/share/man/man1/fastq_quality_trimmer.1 man --recode UTF-8 ./fastq_quality_filter\.1 > fastq_quality_filter\.1\.new chmod 644 fastq_quality_filter.1.new mv -f fastq_quality_filter.1.new fastq_quality_filter.1 man --recode UTF-8 ./fastq_masker\.1 > fastq_masker\.1\.new chmod 644 fastq_masker.1.new mv -f fastq_masker.1.new fastq_masker.1 man --recode UTF-8 ./fastq_quality_trimmer\.1 > fastq_quality_trimmer\.1\.new chmod 644 fastq_quality_trimmer.1.new mv -f fastq_quality_trimmer.1.new fastq_quality_trimmer.1 man --recode UTF-8 ./fastq_quality_converter\.1 > fastq_quality_converter\.1\.new chmod 644 fastq_quality_converter.1.new mv -f fastq_quality_converter.1.new fastq_quality_converter.1 man --recode UTF-8 ./fasta_formatter\.1 > fasta_formatter\.1\.new chmod 644 fasta_formatter.1.new mv -f fasta_formatter.1.new fasta_formatter.1 man --recode UTF-8 ./fasta_nucleotide_changer\.1 > fasta_nucleotide_changer\.1\.new chmod 644 fasta_nucleotide_changer.1.new mv -f fasta_nucleotide_changer.1.new fasta_nucleotide_changer.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='Convert FASTQ files to FASTA files' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_to_fasta > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastq_to_fasta.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTQ/A Artifacts Filter' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_artifacts_filter > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_artifacts_filter.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Clipper' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_clipper > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_clipper.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Collapser' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_collapser > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_collapser.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTX Statistics' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_quality_stats > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_quality_stats.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Renamer' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_renamer > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_renamer.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTQ/A Reverse Complement' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_reverse_complement > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_reverse_complement.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Trimmer' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_trimmer > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_trimmer.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Uncollapser' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_uncollapser > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_uncollapser.1 # Perl scripts add the full path to usage advise which needs to be removed # The script fasta_clipping_histogram.pl does not feature a '-h' option help2man --no-info --no-discard-stderr --version-string='0.0.13.2' -h '' \ --name='Create a Linker Clipping Information Histogram' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fasta_clipping_histogram.pl | \ sed -e 's?^usage: .*\([^/]\+\.pl\)?usage: \1?' \ > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fasta_clipping_histogram.pl.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTX Barcode Splitter' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_barcode_splitter.pl | \ sed -e 's?^usage: .*\([^/]\+\.pl\)?usage: \1?' \ > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_barcode_splitter.pl.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='Solexa-Quality BoxPlot plotter' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastq_quality_boxplot_graph.sh > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastq_quality_boxplot_graph.sh.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Nucleotide Distribution Plotter' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_nucleotide_distribution_graph.sh > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_nucleotide_distribution_graph.sh.1 help2man --no-info --no-discard-stderr --version-string='0.0.13.2' --help-option='-h' \ --name='FASTA/Q Nucleotide Distribution Plotter' \ /«PKGBUILDDIR»/debian/fastx-toolkit/usr/bin/fastx_nucleotide_distribution_line_graph.sh > /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1/fastx_nucleotide_distribution_line_graph.sh.1 for man in `find /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1 "*.1"` ; do cat debian/manpages_see_also >> $man ; done find: `*.1': No such file or directory /bin/sh: 1: cannot create /«PKGBUILDDIR»/debian/fastx-toolkit/usr/share/man/man1: Is a directory make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installcatalogs -a dh_installcron -a dh_installdebconf -a install -o 0 -g 0 -d debian/fastx-toolkit/DEBIAN dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a (grep -s -v perl:Depends debian/fastx-toolkit.substvars; echo perl:Depends=perl) > debian/fastx-toolkit.substvars.new mv debian/fastx-toolkit.substvars.new debian/fastx-toolkit.substvars dh_usrlocal -a dh_link -a rm -f debian/fastx-toolkit/usr/share/doc/fastx-toolkit/NEWS ln -sf changelog debian/fastx-toolkit/usr/share/doc/fastx-toolkit/NEWS dh_compress -a cd debian/fastx-toolkit chmod a-x usr/share/man/man1/fastx_collapser.1 usr/share/man/man1/fastq_quality_filter.1 usr/share/man/man1/fastq_masker.1 usr/share/man/man1/fastx_uncollapser.1 usr/share/man/man1/fastq_quality_trimmer.1 usr/share/man/man1/fastx_reverse_complement.1 usr/share/man/man1/fastx_trimmer.1 usr/share/man/man1/fastq_quality_converter.1 usr/share/man/man1/fasta_clipping_histogram.pl.1 usr/share/man/man1/fastx_artifacts_filter.1 usr/share/man/man1/fastx_nucleotide_distribution_graph.sh.1 usr/share/man/man1/fasta_formatter.1 usr/share/man/man1/fastx_clipper.1 usr/share/man/man1/fastq_quality_boxplot_graph.sh.1 usr/share/man/man1/fastq_to_fasta.1 usr/share/man/man1/fastx_quality_stats.1 usr/share/man/man1/fastx_renamer.1 usr/share/man/man1/fastx_nucleotide_distribution_line_graph.sh.1 usr/share/man/man1/fastx_barcode_splitter.pl.1 usr/share/man/man1/fasta_nucleotide_changer.1 usr/share/doc/fastx-toolkit/changelog.Debian usr/share/doc/fastx-toolkit/changelog usr/share/doc/fastx-toolkit/README gzip -9nf usr/share/man/man1/fastx_collapser.1 usr/share/man/man1/fastq_quality_filter.1 usr/share/man/man1/fastq_masker.1 usr/share/man/man1/fastx_uncollapser.1 usr/share/man/man1/fastq_quality_trimmer.1 usr/share/man/man1/fastx_reverse_complement.1 usr/share/man/man1/fastx_trimmer.1 usr/share/man/man1/fastq_quality_converter.1 usr/share/man/man1/fasta_clipping_histogram.pl.1 usr/share/man/man1/fastx_artifacts_filter.1 usr/share/man/man1/fastx_nucleotide_distribution_graph.sh.1 usr/share/man/man1/fasta_formatter.1 usr/share/man/man1/fastx_clipper.1 usr/share/man/man1/fastq_quality_boxplot_graph.sh.1 usr/share/man/man1/fastq_to_fasta.1 usr/share/man/man1/fastx_quality_stats.1 usr/share/man/man1/fastx_renamer.1 usr/share/man/man1/fastx_nucleotide_distribution_line_graph.sh.1 usr/share/man/man1/fastx_barcode_splitter.pl.1 usr/share/man/man1/fasta_nucleotide_changer.1 usr/share/doc/fastx-toolkit/changelog.Debian usr/share/doc/fastx-toolkit/changelog usr/share/doc/fastx-toolkit/README cd '/«PKGBUILDDIR»' rm -f debian/fastx-toolkit/usr/share/doc/fastx-toolkit/NEWS ln -sf changelog.gz debian/fastx-toolkit/usr/share/doc/fastx-toolkit/NEWS.gz dh_fixperms -a find debian/fastx-toolkit -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/fastx-toolkit ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/fastx-toolkit/usr/share/doc -type f ! -regex 'debian/fastx-toolkit/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastx-toolkit/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/fastx-toolkit/usr/share/man debian/fastx-toolkit/usr/man/ debian/fastx-toolkit/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastx-toolkit -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastx-toolkit/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastx-toolkit/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastx-toolkit -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastx-toolkit/usr/lib/perl5 debian/fastx-toolkit/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/fastx-toolkit/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/fastx-toolkit/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_strip -a strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_quality_stats strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastq_quality_trimmer strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastq_quality_filter strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fasta_formatter strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastq_quality_converter strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_uncollapser strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_clipper strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastq_masker strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_trimmer strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_renamer strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_artifacts_filter strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastq_to_fasta strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_collapser strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fastx_reverse_complement strip --remove-section=.comment --remove-section=.note debian/fastx-toolkit/usr/bin/fasta_nucleotide_changer dh_makeshlibs -a rm -f debian/fastx-toolkit/DEBIAN/shlibs dh_shlibdeps -a dpkg-shlibdeps -Tdebian/fastx-toolkit.substvars debian/fastx-toolkit/usr/bin/fastx_quality_stats debian/fastx-toolkit/usr/bin/fastq_quality_trimmer debian/fastx-toolkit/usr/bin/fastq_quality_filter debian/fastx-toolkit/usr/bin/fasta_formatter debian/fastx-toolkit/usr/bin/fastq_quality_converter debian/fastx-toolkit/usr/bin/fastx_uncollapser debian/fastx-toolkit/usr/bin/fastx_clipper debian/fastx-toolkit/usr/bin/fastq_masker debian/fastx-toolkit/usr/bin/fastx_trimmer debian/fastx-toolkit/usr/bin/fastx_renamer debian/fastx-toolkit/usr/bin/fastx_artifacts_filter debian/fastx-toolkit/usr/bin/fastq_to_fasta debian/fastx-toolkit/usr/bin/fastx_collapser debian/fastx-toolkit/usr/bin/fastx_reverse_complement debian/fastx-toolkit/usr/bin/fasta_nucleotide_changer dpkg-shlibdeps: warning: debian/fastx-toolkit/usr/bin/fastx_uncollapser contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/fastx-toolkit/usr/bin/fasta_formatter contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/fastx-toolkit.substvars dpkg-gencontrol -ldebian/changelog -Tdebian/fastx-toolkit.substvars -Pdebian/fastx-toolkit dpkg-gencontrol: warning: package fastx-toolkit: unused substitution variable ${perl:Depends} chmod 644 debian/fastx-toolkit/DEBIAN/control chown 0:0 debian/fastx-toolkit/DEBIAN/control dh_md5sums -a (cd debian/fastx-toolkit >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/fastx-toolkit/DEBIAN/md5sums chown 0:0 debian/fastx-toolkit/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/fastx-toolkit .. dpkg-deb: building package `fastx-toolkit' in `../fastx-toolkit_0.0.13.2-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../fastx-toolkit_0.0.13.2-1_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 fastx-toolkit-0.0.13.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120527-1949 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ fastx-toolkit_0.0.13.2-1_armhf.changes: ─────────────────────────────────────── Format: 1.8 Date: Tue, 15 May 2012 21:02:22 +0900 Source: fastx-toolkit Binary: fastx-toolkit Architecture: armhf Version: 0.0.13.2-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Charles Plessy Description: fastx-toolkit - FASTQ/A short nucleotide reads pre-processing tools Changes: fastx-toolkit (0.0.13.2-1) unstable; urgency=low . 1313f16 Imported Upstream version 0.0.13.2 dbfb3ae Removed debian/patches/gcc-4.7.patch, applied upstream. 182cd30 Include 7 digits of the commit ID in the changelog entry. 2ae7b63 Spellchecked common “See also” section of the manpages. 363856c Verbose Debhelper. Checksums-Sha1: a8a1ef8c8cd7f429340175b0c5e3c179b37b393c 139910 fastx-toolkit_0.0.13.2-1_armhf.deb Checksums-Sha256: 5dc2af5cb0b3e7e3ceed187a9c1a9199ad34967f56d3fbf1521574b634ca8eeb 139910 fastx-toolkit_0.0.13.2-1_armhf.deb Files: d2bac52c421291549efce76f746cecda 139910 science optional fastx-toolkit_0.0.13.2-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ fastx-toolkit_0.0.13.2-1_armhf.deb ────────────────────────────────── new debian package, version 2.0. size 139910 bytes: control archive= 2150 bytes. 1082 bytes, 19 lines control 3342 bytes, 46 lines md5sums Package: fastx-toolkit Version: 0.0.13.2-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 466 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libgtextutils0 (>= 0.6.2), libstdc++6 (>= 4.6), libgd-graph-perl, libperlio-gzip-perl Section: science Priority: optional Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Description: FASTQ/A short nucleotide reads pre-processing tools The FASTX-Toolkit is a collection of command line tools for preprocessing short nucleotide reads in FASTA and FASTQ formats, usually produced by Next-Generation sequencing machines. The main processing of such FASTA/FASTQ files is mapping (aligning) the sequences to reference genomes or other databases using specialized programs like BWA, Bowtie and many others. However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome—manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks. drwxr-xr-x root/root 0 2012-05-27 19:48 ./ drwxr-xr-x root/root 0 2012-05-27 19:47 ./usr/ drwxr-xr-x root/root 0 2012-05-27 19:48 ./usr/share/ drwxr-xr-x root/root 0 2012-05-27 19:48 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-27 19:48 ./usr/share/man/man1/ -rw-r--r-- root/root 505 2012-05-27 19:48 ./usr/share/man/man1/fastx_collapser.1.gz -rw-r--r-- root/root 599 2012-05-27 19:48 ./usr/share/man/man1/fastx_artifacts_filter.1.gz -rw-r--r-- root/root 589 2012-05-27 19:48 ./usr/share/man/man1/fastx_uncollapser.1.gz -rw-r--r-- root/root 557 2012-05-27 19:48 ./usr/share/man/man1/fastx_renamer.1.gz -rw-r--r-- root/root 661 2012-05-27 19:48 ./usr/share/man/man1/fastq_to_fasta.1.gz -rw-r--r-- root/root 518 2012-05-27 19:48 ./usr/share/man/man1/fastx_reverse_complement.1.gz -rw-r--r-- root/root 659 2012-05-27 19:48 ./usr/share/man/man1/fastq_quality_filter.1.gz -rw-r--r-- root/root 558 2012-05-27 19:48 ./usr/share/man/man1/fastq_quality_converter.1.gz -rw-r--r-- root/root 583 2012-05-27 19:48 ./usr/share/man/man1/fastx_nucleotide_distribution_graph.sh.1.gz -rw-r--r-- root/root 638 2012-05-27 19:48 ./usr/share/man/man1/fastx_trimmer.1.gz -rw-r--r-- root/root 904 2012-05-27 19:48 ./usr/share/man/man1/fastx_clipper.1.gz -rw-r--r-- root/root 922 2012-05-27 19:48 ./usr/share/man/man1/fasta_formatter.1.gz -rw-r--r-- root/root 728 2012-05-27 19:48 ./usr/share/man/man1/fastq_quality_trimmer.1.gz -rw-r--r-- root/root 645 2012-05-27 19:48 ./usr/share/man/man1/fasta_nucleotide_changer.1.gz -rw-r--r-- root/root 613 2012-05-27 19:48 ./usr/share/man/man1/fastq_quality_boxplot_graph.sh.1.gz -rw-r--r-- root/root 929 2012-05-27 19:48 ./usr/share/man/man1/fastx_quality_stats.1.gz -rw-r--r-- root/root 688 2012-05-27 19:48 ./usr/share/man/man1/fastq_masker.1.gz -rw-r--r-- root/root 468 2012-05-27 19:48 ./usr/share/man/man1/fasta_clipping_histogram.pl.1.gz -rw-r--r-- root/root 2197 2012-05-27 19:48 ./usr/share/man/man1/fastx_barcode_splitter.pl.1.gz -rw-r--r-- root/root 590 2012-05-27 19:48 ./usr/share/man/man1/fastx_nucleotide_distribution_line_graph.sh.1.gz drwxr-xr-x root/root 0 2012-05-27 19:47 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-27 19:48 ./usr/share/doc/fastx-toolkit/ -rw-r--r-- root/root 3728 2012-04-12 13:02 ./usr/share/doc/fastx-toolkit/README.gz -rw-r--r-- root/root 802 2012-05-15 05:02 ./usr/share/doc/fastx-toolkit/changelog.Debian.gz -rw-r--r-- root/root 37701 2012-05-14 20:43 ./usr/share/doc/fastx-toolkit/copyright -rw-r--r-- root/root 425 2012-04-12 13:02 ./usr/share/doc/fastx-toolkit/changelog.gz -rw-r--r-- root/root 482 2012-05-14 20:39 ./usr/share/doc/fastx-toolkit/README.Debian -rw-r--r-- root/root 372 2012-04-12 13:02 ./usr/share/doc/fastx-toolkit/THANKS drwxr-xr-x root/root 0 2012-05-27 19:48 ./usr/bin/ -rwxr-xr-x root/root 22072 2012-05-27 19:48 ./usr/bin/fastx_quality_stats -rwxr-xr-x root/root 22052 2012-05-27 19:48 ./usr/bin/fastq_quality_trimmer -rwxr-xr-x root/root 22048 2012-05-27 19:48 ./usr/bin/fastq_quality_filter -rwxr-xr-x root/root 5896 2012-05-27 19:47 ./usr/bin/fastx_nucleotide_distribution_graph.sh -rwxr-xr-x root/root 18036 2012-05-27 19:48 ./usr/bin/fasta_formatter -rwxr-xr-x root/root 17948 2012-05-27 19:48 ./usr/bin/fastq_quality_converter -rwxr-xr-x root/root 13925 2012-05-27 19:47 ./usr/bin/fastx_barcode_splitter.pl -rwxr-xr-x root/root 34568 2012-05-27 19:48 ./usr/bin/fastx_uncollapser -rwxr-xr-x root/root 55104 2012-05-27 19:48 ./usr/bin/fastx_clipper -rwxr-xr-x root/root 5380 2012-05-27 19:47 ./usr/bin/fastq_quality_boxplot_graph.sh -rwxr-xr-x root/root 17952 2012-05-27 19:48 ./usr/bin/fastq_masker -rwxr-xr-x root/root 17952 2012-05-27 19:48 ./usr/bin/fastx_trimmer -rwxr-xr-x root/root 17956 2012-05-27 19:48 ./usr/bin/fastx_renamer -rwxr-xr-x root/root 17948 2012-05-27 19:48 ./usr/bin/fastx_artifacts_filter -rwxr-xr-x root/root 17956 2012-05-27 19:48 ./usr/bin/fastq_to_fasta -rwxr-xr-x root/root 30420 2012-05-27 19:48 ./usr/bin/fastx_collapser -rwxr-xr-x root/root 17948 2012-05-27 19:48 ./usr/bin/fastx_reverse_complement -rwxr-xr-x root/root 2764 2012-05-27 19:47 ./usr/bin/fasta_clipping_histogram.pl -rwxr-xr-x root/root 6069 2012-05-27 19:47 ./usr/bin/fastx_nucleotide_distribution_line_graph.sh -rwxr-xr-x root/root 17944 2012-05-27 19:48 ./usr/bin/fasta_nucleotide_changer lrwxrwxrwx root/root 0 2012-05-27 19:48 ./usr/share/doc/fastx-toolkit/NEWS.gz -> changelog.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: autotools-dev* bsdmainutils* debhelper* file* fontconfig-config* gettext* gettext-base* groff-base* help2man* html2text* intltool-debian* libcroco3* libexpat1* libffi5* libfontconfig1* libfreetype6* libgd-gd2-perl* libgd-graph-perl* libgd-text-perl* libgd2-xpm* libglib2.0-0* libgtextutils-dev* libgtextutils0* libjpeg8* libmagic1* libpcre3* libperlio-gzip-perl* libpipeline1* libpng12-0* libpopt0* libunistring0* libx11-6* libx11-data* libxau6* libxcb1* libxdmcp6* libxml2* libxpm4* man-db* pkg-config* po-debconf* sbuild-build-depends-core-dummy* sbuild-build-depends-fastx-toolkit-dummy* ttf-dejavu-core* 0 upgraded, 0 newly installed, 44 to remove and 18 not upgraded. After this operation, 36.5 MB disk space will be freed. 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Removing ttf-dejavu-core ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 8796 Build-Time: 221 Distribution: testing Install-Time: 97 Job: fastx-toolkit_0.0.13.2-1 Package: fastx-toolkit Package-Time: 366 Source-Version: 0.0.13.2-1 Space: 8796 Status: successful Version: 0.0.13.2-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120527-1949 Build needed 00:06:06, 8796k disc space