sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ theseus 1.6.2-2 (armhf) 18 Jun 2012 04:58 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: theseus Version: 1.6.2-2 Source Version: 1.6.2-2 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/theseus-47kCae/theseus-1.6.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/theseus-47kCae' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-d3463ffc-61ee-4dbb-bf12-09687ba2dac4' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main Translation-en 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: 'theseus' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/theseus/trunk/ Need to get 1230 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main theseus 1.6.2-2 (dsc) [1361 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main theseus 1.6.2-2 (tar) [1215 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main theseus 1.6.2-2 (diff) [14.2 kB] Fetched 1230 kB in 0s (3319 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-HrSglC/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 2 not upgraded. Need to get 0 B/702 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 ... 10659 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), libgsl0-dev Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libgsl0-dev dpkg-deb: building package `sbuild-build-depends-theseus-dummy' in `/«BUILDDIR»/resolver-7ZfWDY/apt_archive/sbuild-build-depends-theseus-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install theseus build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libgsl0-dev libgsl0ldbl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html 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: bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libgsl0-dev libgsl0ldbl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-theseus-dummy 0 upgraded, 23 newly installed, 0 to remove and 2 not upgraded. Need to get 2036 kB/11.5 MB of archives. After this operation, 30.8 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main libgsl0ldbl armhf 1.15+dfsg-1 [904 kB] Get:2 http://repo.raspbian.lan/raspbian/ testing/main libgsl0-dev armhf 1.15+dfsg-1 [1132 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2036 kB in 0s (3515 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10659 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 libasprintf0c2:armhf. Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-8_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_2.8.0+dfsg1-3_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 libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package libgettextpo0:armhf. Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-8_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-8_armhf.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-8_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120528_all.deb) ... Selecting previously unselected package libgsl0ldbl. Unpacking libgsl0ldbl (from .../libgsl0ldbl_1.15+dfsg-1_armhf.deb) ... Selecting previously unselected package libgsl0-dev. Unpacking libgsl0-dev (from .../libgsl0-dev_1.15+dfsg-1_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-theseus-dummy. Unpacking sbuild-build-depends-theseus-dummy (from .../sbuild-build-depends-theseus-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libasprintf0c2:armhf (0.18.1.1-8) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.8.0+dfsg1-3) ... 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 libunistring0:armhf (0.9.3-5) ... Setting up libgettextpo0:armhf (0.18.1.1-8) ... Setting up bsdmainutils (9.0.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-8) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-8) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120528) ... Setting up libgsl0ldbl (1.15+dfsg-1) ... Setting up libgsl0-dev (1.15+dfsg-1) ... Setting up sbuild-build-depends-theseus-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.3 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-33 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.18-1 Package versions: apt_0.9.3+rpi1 base-files_6.9 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.2 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120528 debian-archive-keyring_2012.3 debianutils_4.3.1 diffutils_1:3.2-6 dpkg_1.16.3 dpkg-dev_1.16.3 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-8 gettext-base_0.18.1.1-8 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-7 gzip_1.4-5 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 libapt-pkg4.12_0.9.3+rpi1 libasprintf0c2_0.18.1.1-8 libattr1_1:2.4.46-7 libblkid1_2.20.1-5 libbz2-1.0_1.0.6-1 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.3 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libgettextpo0_0.18.1.1-8 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.0-1.1+rpi libgsl0-dev_1.15+dfsg-1 libgsl0ldbl_1.15+dfsg-1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-8 libncursesw5_5.9-8 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 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_5.9-8 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-5 libxml2_2.8.0+dfsg1-3 linux-libc-dev_3.2.18-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian6 make_3.81-8.2 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-5 multiarch-support_2.13-33 ncurses-base_5.9-7 ncurses-bin_5.9-8 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 raspbian-archive-keyring_20120528.2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-theseus-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-11 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jun 8 06:58:52 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./theseus_1.6.2-2.dsc dpkg-source: info: extracting theseus in theseus-1.6.2 dpkg-source: info: unpacking theseus_1.6.2.orig.tar.gz dpkg-source: info: unpacking theseus_1.6.2-2.debian.tar.gz dpkg-source: info: applying 10_kbsd.patch dpkg-source: info: applying 20_hardening.patch dpkg-source: info: applying 20_exclude_apple_options.patch dpkg-source: info: applying 21_use_dpkg_buildflags.patch dpkg-source: info: applying 22_hardening_compile.patch 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-d3463ffc-61ee-4dbb-bf12-09687ba2dac4 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package theseus dpkg-buildpackage: source version 1.6.2-2 dpkg-source --before-build theseus-1.6.2 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' find . -name '*.[oa]' -exec rm -f {} \; rm -f theseus &> /dev/null make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»' ( cd libdistfit; make && cp libdistfit.a ../lib ) make[2]: Entering directory `/«PKGBUILDDIR»/libdistfit' /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c statistics.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c beta_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c betaprime_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c betasym_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c binomial_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c cauchy_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c chi_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c chisqr_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c chisqrgen_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c EVD_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c exp_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c gamma_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c invchisqr_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c invgamma_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c invgauss_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c laplace_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c logistic_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c lognormal_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c maxwell_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c negbinom_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c normal_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c pareto_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c rayleigh_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c recinvgauss_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c uniform_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c vonmises_dist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c weibull_dist.c ar -rvs libdistfit.a statistics.o beta_dist.o betaprime_dist.o betasym_dist.o binomial_dist.o cauchy_dist.o chi_dist.o chisqr_dist.o chisqrgen_dist.o EVD_dist.o exp_dist.o gamma_dist.o invchisqr_dist.o invgamma_dist.o invgauss_dist.o laplace_dist.o logistic_dist.o lognormal_dist.o maxwell_dist.o negbinom_dist.o normal_dist.o pareto_dist.o rayleigh_dist.o recinvgauss_dist.o uniform_dist.o vonmises_dist.o weibull_dist.o ar: creating libdistfit.a a - statistics.o a - beta_dist.o a - betaprime_dist.o a - betasym_dist.o a - binomial_dist.o a - cauchy_dist.o a - chi_dist.o a - chisqr_dist.o a - chisqrgen_dist.o a - EVD_dist.o a - exp_dist.o a - gamma_dist.o a - invchisqr_dist.o a - invgamma_dist.o a - invgauss_dist.o a - laplace_dist.o a - logistic_dist.o a - lognormal_dist.o a - maxwell_dist.o a - negbinom_dist.o a - normal_dist.o a - pareto_dist.o a - rayleigh_dist.o a - recinvgauss_dist.o a - uniform_dist.o a - vonmises_dist.o a - weibull_dist.o ranlib libdistfit.a make[2]: Leaving directory `/«PKGBUILDDIR»/libdistfit' ( cd libDLTutils; make && cp libDLTutils.a ../lib ) make[2]: Entering directory `/«PKGBUILDDIR»/libDLTutils' /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c DLTutils.c ar -rvs libDLTutils.a DLTutils.o ar: creating libDLTutils.a a - DLTutils.o ranlib libDLTutils.a make[2]: Leaving directory `/«PKGBUILDDIR»/libDLTutils' ( cd libmsa; make && cp libmsa.a ../lib ) make[2]: Entering directory `/«PKGBUILDDIR»/libmsa' /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c msa.c msa.c: In function 'readphylipd': msa.c:2212:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c: In function 'readphylip': msa.c:2109:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c:2129:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c:2155:18: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c: In function 'readaln': msa.c:1326:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c:1389:14: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c:1416:18: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c: In function 'ismsf': msa.c:181:14: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c: In function 'isnexdist': msa.c:147:14: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] msa.c: In function 'getmsa': msa.c:80:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] ar -rvs libmsa.a msa.o ar: creating libmsa.a a - msa.o ranlib libmsa.a make[2]: Leaving directory `/«PKGBUILDDIR»/libmsa' ( cd libdltmath; make && cp libdltmath.a ../lib ) make[2]: Entering directory `/«PKGBUILDDIR»/libdltmath' /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c ludcmp.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c MatUtils.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c Mat3Utils.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c Mat4Utils.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c VecUtils.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c quicksort.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c integrate.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c eigen_gsl.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c eigen.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c MultivarGamma.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c specfunc.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c RegGamma.c ar -rvs libdltmath.a ludcmp.o MatUtils.o Mat3Utils.o Mat4Utils.o VecUtils.o quicksort.o integrate.o eigen_gsl.o eigen.o MultivarGamma.o specfunc.o RegGamma.o ar: creating libdltmath.a a - ludcmp.o a - MatUtils.o a - Mat3Utils.o a - Mat4Utils.o a - VecUtils.o a - quicksort.o a - integrate.o a - eigen_gsl.o a - eigen.o a - MultivarGamma.o a - specfunc.o a - RegGamma.o ranlib libdltmath.a make[2]: Leaving directory `/«PKGBUILDDIR»/libdltmath' ( cd libdssplite; make && cp libdssplite.a ../lib ) make[2]: Entering directory `/«PKGBUILDDIR»/libdssplite' /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c dssplite.c ar -rvs libdssplite.a dssplite.o ar: creating libdssplite.a a - dssplite.o ranlib libdssplite.a make[2]: Leaving directory `/«PKGBUILDDIR»/libdssplite' /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c CovMat.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c DistMat.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c Embed.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c Error.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c FragCds.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c FragDist.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c HierarchVars.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c lodmats.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c MultiPose.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c MultiPose2MSA.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c MultiPoseMix.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c PCAstats.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c pdbIO.c pdbIO.c: In function 'ReadBinMatrix': pdbIO.c:1942:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1943:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1944:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c: In function 'ReadBinPDBCds': pdbIO.c:1898:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1901:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1902:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1904:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1906:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1907:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1908:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1909:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1910:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1911:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1912:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1913:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1914:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1915:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1916:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1917:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1919:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1920:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1921:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1922:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1923:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1924:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c: In function 'ReadBinPDBCdsArray': pdbIO.c:1827:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1837:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] pdbIO.c:1838:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c pdbMalloc.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c pdbStats.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c pdbUtils.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c QuarticHornFrag.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c RandCds.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c pdbSSM.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c ProcGSLSVD.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c ProcGSLSVDOcc.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c ProcJacobiSVD.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c GibbsMet.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c qcprot.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c termcol.c /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c theseuslib.c ar -rvs libtheseus.a CovMat.o DistMat.o Embed.o Error.o FragCds.o FragDist.o HierarchVars.o lodmats.o MultiPose.o MultiPose2MSA.o MultiPoseMix.o PCAstats.o pdbIO.o pdbMalloc.o pdbStats.o pdbUtils.o QuarticHornFrag.o RandCds.o pdbSSM.o ProcGSLSVD.o ProcGSLSVDOcc.o ProcJacobiSVD.o GibbsMet.o qcprot.o termcol.o theseuslib.o ar: creating libtheseus.a a - CovMat.o a - DistMat.o a - Embed.o a - Error.o a - FragCds.o a - FragDist.o a - HierarchVars.o a - lodmats.o a - MultiPose.o a - MultiPose2MSA.o a - MultiPoseMix.o a - PCAstats.o a - pdbIO.o a - pdbMalloc.o a - pdbStats.o a - pdbUtils.o a - QuarticHornFrag.o a - RandCds.o a - pdbSSM.o a - ProcGSLSVD.o a - ProcGSLSVDOcc.o a - ProcJacobiSVD.o a - GibbsMet.o a - qcprot.o a - termcol.o a - theseuslib.o mv libtheseus.a lib/libtheseus.a ranlib lib/libtheseus.a /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -c theseus.c theseus.c: In function 'ConvertLele': theseus.c:1275:18: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] theseus.c: In function 'ConvertDryden': theseus.c:1189:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] theseus.c:1197:15: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 -D_FORTIFY_SOURCE=2 -Wl,-z,relro -L./lib theseus.o CovMat.o DistMat.o Embed.o Error.o FragCds.o FragDist.o HierarchVars.o lodmats.o MultiPose.o MultiPose2MSA.o MultiPoseMix.o PCAstats.o pdbIO.o pdbMalloc.o pdbStats.o pdbUtils.o QuarticHornFrag.o RandCds.o pdbSSM.o ProcGSLSVD.o ProcGSLSVDOcc.o ProcJacobiSVD.o GibbsMet.o qcprot.o termcol.o theseuslib.o -lgsl -lgslcblas -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus -lpthread -o theseus make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' # Fix wrong path used in upstream script. Fixing it here is safer than # changing the patch for any new upstream release sed -e 's?/usr/local/bin?/usr/bin?' \ -e 's?/usr/bin/sed?/bin/sed?' \ theseus_align > debian/theseus/usr/bin/theseus_align make[1]: Leaving directory `/«PKGBUILDDIR»' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/theseus/usr/bin/theseus was not linked against libgslcblas.so.0 (it uses none of the library's symbols). dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `theseus' in `../theseus_1.6.2-2_armhf.deb'. dpkg-genchanges -B -mbuildd >../theseus_1.6.2-2_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 theseus-1.6.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120618-0506 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ theseus_1.6.2-2_armhf.changes: ────────────────────────────── Format: 1.8 Date: Fri, 08 Jun 2012 08:45:38 +0200 Source: theseus Binary: theseus Architecture: armhf Version: 1.6.2-2 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: theseus - superimpose macromolecules using maximum likelihood Closes: 668120 Changes: theseus (1.6.2-2) unstable; urgency=low . * debian/upstream: Added missing space, fixed Name * debian/patches: Two patches from Simon Ruderich to enable hardening (thanks to Simon) Closes: #668120 Checksums-Sha1: d329966a27bdcede459cb4ba9bf4d64057ecc7ea 1185774 theseus_1.6.2-2_armhf.deb Checksums-Sha256: 5797e6d464417d97afb18cc860e3049ceb677ab019930062000b8dfc7511be61 1185774 theseus_1.6.2-2_armhf.deb Files: f8ba08cb8a3d206523c33c35e1b27144 1185774 science optional theseus_1.6.2-2_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ theseus_1.6.2-2_armhf.deb ───────────────────────── new debian package, version 2.0. size 1185774 bytes: control archive= 1447 bytes. 1026 bytes, 22 lines control 1703 bytes, 23 lines md5sums Package: theseus Version: 1.6.2-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1668 Depends: libc6 (>= 2.13-28), libgsl0ldbl (>= 1.9), muscle Suggests: clustlaw, mafft, t-coffee, kalign, dialign Section: science Priority: optional Homepage: http://www.theseus3d.org Description: superimpose macromolecules using maximum likelihood Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By down-weighting variable regions of the superposition and by correcting for correlations among atoms, the ML superposition method produces very accurate structural alignments. . When macromolecules with different residue sequences are superimposed, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel superimposition algorithm that includes all of the data. drwxr-xr-x root/root 0 2012-06-18 05:05 ./ drwxr-xr-x root/root 0 2012-06-18 05:05 ./usr/ drwxr-xr-x root/root 0 2012-06-18 05:05 ./usr/share/ drwxr-xr-x root/root 0 2012-06-18 05:05 ./usr/share/man/ drwxr-xr-x root/root 0 2012-06-18 05:05 ./usr/share/man/man1/ -rw-r--r-- root/root 7777 2012-06-18 05:05 ./usr/share/man/man1/theseus.1.gz -rw-r--r-- root/root 1385 2012-06-18 05:05 ./usr/share/man/man1/theseus_align.1.gz drwxr-xr-x root/root 0 2012-06-18 05:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-06-18 05:05 ./usr/share/doc/theseus/ -rw-r--r-- root/root 2327 2012-06-07 23:46 ./usr/share/doc/theseus/changelog.Debian.gz -rw-r--r-- root/root 4690 2012-03-24 14:51 ./usr/share/doc/theseus/copyright drwxr-xr-x root/root 0 2012-06-18 05:06 ./usr/share/doc/theseus/examples/ -rw-r--r-- root/root 1642 2011-11-03 11:45 ./usr/share/doc/theseus/examples/cytc.aln -rw-r--r-- root/root 19115 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1yeb__.pdb.gz -rw-r--r-- root/root 18807 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d2pcbb_.pdb.gz -rw-r--r-- root/root 1576 2008-11-18 22:28 ./usr/share/doc/theseus/examples/getexamples -rw-r--r-- root/root 17493 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1kyow_.pdb.gz -rw-r--r-- root/root 1346 2011-11-03 11:45 ./usr/share/doc/theseus/examples/README -rw-r--r-- root/root 199 2011-11-03 11:45 ./usr/share/doc/theseus/examples/cytc.filemap -rw-r--r-- root/root 18950 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1cih__.pdb.gz -rw-r--r-- root/root 17321 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1u74d_.pdb.gz -rw-r--r-- root/root 19001 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1csx__.pdb.gz -rw-r--r-- root/root 27825 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1m60a_.pdb.gz -rw-r--r-- root/root 16205 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1lfma_.pdb.gz -rw-r--r-- root/root 19250 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1crj__.pdb.gz -rw-r--r-- root/root 19091 2011-11-03 11:45 ./usr/share/doc/theseus/examples/d1csu__.pdb.gz -rw-r--r-- root/root 572182 2011-11-03 11:45 ./usr/share/doc/theseus/examples/1s40.pdb.gz -rw-r--r-- root/root 468 2009-08-31 06:15 ./usr/share/doc/theseus/README.Debian -rw-r--r-- root/root 1483 2008-11-17 22:38 ./usr/share/doc/theseus/citation.bib drwxr-xr-x root/root 0 2012-06-18 05:06 ./usr/bin/ -rwxr-xr-x root/root 6634 2012-06-18 05:05 ./usr/bin/theseus_align -rwxr-xr-x root/root 871392 2012-06-18 05:06 ./usr/bin/theseus ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* file* gettext* gettext-base* groff-base* html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5* libgettextpo0* libglib2.0-0* libgsl0-dev* libgsl0ldbl* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* sbuild-build-depends-core-dummy* sbuild-build-depends-theseus-dummy* 0 upgraded, 0 newly installed, 24 to remove and 2 not upgraded. After this operation, 30.8 MB disk space will be freed. (Reading database ... 12291 files and directories currently installed.) Removing sbuild-build-depends-theseus-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libasprintf0c2:armhf ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libgettextpo0:armhf ... Removing libgsl0-dev ... Removing libgsl0ldbl ... Purging configuration files for libgsl0ldbl ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 19128 Build-Time: 378 Distribution: testing Install-Time: 69 Job: theseus_1.6.2-2 Package: theseus Package-Time: 467 Source-Version: 1.6.2-2 Space: 19128 Status: successful Version: 1.6.2-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120618-0506 Build needed 00:07:47, 19128k disc space