DC-Build-Header: plink 1.07-1 / Fri Jan 13 00:56:26 +0100 2012 Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-26.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ plink 1.07-1 (amd64) 13 Jan 2012 00:58 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: plink Version: 1.07-1 Source Version: 1.07-1 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 3s (5197 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'plink' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/ Need to get 584 kB of source archives. Get:1 http://localhost/debian/ sid/main plink 1.07-1 (dsc) [1304 B] Get:2 http://localhost/debian/ sid/main plink 1.07-1 (tar) [577 kB] Get:3 http://localhost/debian/ sid/main plink 1.07-1 (diff) [5596 B] Fetched 584 kB in 0s (7361 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 `/build/plink-FKyQ9t/resolver-5TTydR/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 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 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) ... Cannot open /var/lib/schroot/mount/lsid64b-39b066c2-f17d-49a2-8ab6-1016e5a94b23/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), quilt, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), quilt, zlib1g-dev dpkg-deb: building package `sbuild-build-depends-plink-dummy' in `/build/plink-FKyQ9t/resolver-AREeiT/apt_archive/sbuild-build-depends-plink-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install plink 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 diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent 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 diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-plink-dummy zlib1g-dev 0 upgraded, 21 newly installed, 0 to remove and 10 not upgraded. Need to get 10.1 MB/10.1 MB of archives. After this operation, 27.3 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 libglib2.0-0 libxml2 libcroco3 libunistring0 bsdmainutils groff-base man-db libmagic1 file gettext-base html2text gettext intltool-debian po-debconf debhelper diffstat quilt zlib1g-dev sbuild-build-depends-plink-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:4 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:5 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:6 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:7 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:8 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:9 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:10 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:11 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:12 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:13 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:15 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:18 http://localhost/debian/ sid/main diffstat amd64 1.55-2 [29.9 kB] Get:19 http://localhost/debian/ sid/main quilt all 0.50-2 [381 kB] Get:20 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Preconfiguring packages ... Fetched 10.1 MB in 0s (41.4 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.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_8.9.14_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-2_amd64.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ... Selecting previously unselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-plink-dummy. Unpacking sbuild-build-depends-plink-dummy (from .../sbuild-build-depends-plink-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libpcre3 (8.12-4) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up bsdmainutils (8.2.3) ... 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 (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up diffstat (1.55-2) ... Setting up quilt (0.50-2) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ... Setting up sbuild-build-depends-plink-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 clang_3.0-5 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 libllvm3.0_3.0-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 quilt_0.50-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-plink-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Oct 23 14:33:43 2009 CEST using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./plink_1.07-1.dsc dpkg-source: info: extracting plink in plink-1.07 dpkg-source: info: unpacking plink_1.07.orig.tar.gz dpkg-source: info: applying plink_1.07-1.diff.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package plink dpkg-buildpackage: source version 1.07-1 dpkg-source --before-build plink-1.07 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean QUILT_PATCHES=debian/patches \ quilt --quiltrc /dev/null pop -a -R || test $? = 2 No patch removed rm -rf .pc debian/stamp-patched dh_testdir dh_testroot /usr/bin/make clean make[1]: Entering directory `/build/plink-FKyQ9t/plink-1.07' rm -f *.o *~ make[1]: Leaving directory `/build/plink-FKyQ9t/plink-1.07' dh_clean build-stamp install-stamp plink dpkg-source -b plink-1.07 dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1) dpkg-source: info: using source format `1.0' dpkg-source: info: building plink using existing plink_1.07.orig.tar.gz dpkg-source: info: building plink in plink_1.07-1.diff.gz dpkg-source: warning: ignoring deletion of file blox.cpp~ dpkg-source: warning: ignoring deletion of file webcheck.cpp~ dpkg-source: info: building plink in plink_1.07-1.dsc debian/rules build /usr/bin/make CXXFLAGS='-Wall -g -O2 -DWITH_R_PLUGINS -DUNIX' FORCE_DYNAMIC=1 QUILT_PATCHES=debian/patches \ quilt --quiltrc /dev/null push -a || test $? = 2 make[1]: Entering directory `/build/plink-FKyQ9t/plink-1.07' g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c plink.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c options.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c input.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c binput.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tinput.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genome.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c helper.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c stats.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c filters.cpp Applying patch 30_endiandetection.patch patching file Rsrv.h Hunk #1 succeeded at 321 (offset 8 lines). Now at patch 30_endiandetection.patch touch debian/stamp-patched g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c locus.cpp genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] int geno_nm = 0; ^ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] double tothet = 0; ^ filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] int nm; ^ filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] double freq; ^ stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteSNPs(del); ^ genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^ helper.cpp:219:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] double e10 = E10*S; ^ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] double e20 = E20*S; ^ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] double e21 = E21*S; ^ helper.cpp:232:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:244:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:256:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ genome.cpp:1067:23: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~^~~~~~~~ ~~ genome.cpp:1067:23: note: place parentheses around the '&&' expression to silence this warning if ( (!par::silent ) && c==c2 || c==np) ^ ( ) helper.cpp:380:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:393:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:407:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] int win_end = win_start + par::prune_ld_win; ^ filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] int x = 0; ^ plink.cpp:763:26: warning: '&&' within '||' [-Wlogical-op-parentheses] par::make_founders && ~~~~~~~~~~~~~~~~~~~^~ plink.cpp:763:26: note: place parentheses around the '&&' expression to silence this warning par::make_founders && ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c multi.cpp input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] bool success = false; ^ helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] set * s; ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c crandom.cpp helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] int last = -1; ^ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] int thisChromosome = P.locus[0]->chr; ^ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] int nextChromosome; ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cluster.cpp multi.cpp:154:8: warning: unused variable 'is0zero' [-Wunused-variable] bool is0zero = IBDg.z0 < EPS ? true : false; ^ multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] bool is1zero = IBDg.z1 < EPS ? true : false; ^ cluster.cpp:492:8: warning: unused variable 'size' [-Wunused-variable] int size = peeps.size(); ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mds.cpp 4 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c output.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c informative.cpp mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] bool flag = svd(D,eigenvalue,eigenvector); ^ 8 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c assoc.cpp output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] int n_removed = deleteIndividuals(del); ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c epi.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c prephap.cpp assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^ 4 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c phase.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c trio.cpp epi.cpp:438:12: warning: unused variable 'zero' [-Wunused-variable] double zero = 0; ^ epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] int c=0; ^ trio.cpp:252:26: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if ( mf->kid.size()>=0) ~~~~~~~~~~~~~~^ ~ trio.cpp:931:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteSNPs(mendel_locus); ^ trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteIndividuals(indel); ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tdt.cpp tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sharing.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genepi.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sets.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c perm.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mh.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genedrop.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c gxe.cpp genepi.cpp:78:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ genepi.cpp:169:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ genepi.cpp:506:10: warning: unused variable 'n12' [-Wunused-variable] int n12 = n1 + n2; ^ genepi.cpp:507:10: warning: unused variable 'ne' [-Wunused-variable] int ne = n1 < n2 ? n1 : n2; ^ genepi.cpp:1043:10: warning: unused variable 'n12' [-Wunused-variable] int n12 = n1 + n2; ^ genepi.cpp:1044:10: warning: unused variable 'ne' [-Wunused-variable] int ne = n1 < n2 ? n1 : n2;// ne = min(p,q) ^ genepi.cpp:1064:10: warning: unused variable 'nind' [-Wunused-variable] int nind = calcGENEPIMeanVariance(pSNP, ^ genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] bool casewise_deletion = false; ^ sets.cpp:771:37: error: redefinition of 'i' with a different type vector::iterator i = PP->sample.begin(); ^ sets.cpp:703:12: note: previous definition is here for (int i=0; i > >')) while ( i != PP->sample.end() ) ~ ^ ~~~~~~~~~~~~~~~~ /usr/include/c++/4.6/bits/postypes.h:222:5: note: candidate template ignored: failed template argument deduction operator!=(const fpos<_StateT>& __lhs, const fpos<_StateT>& __rhs) ^ /usr/include/c++/4.6/bits/stl_pair.h:214:5: note: candidate template ignored: failed template argument deduction operator!=(const pair<_T1, _T2>& __x, const pair<_T1, _T2>& __y) ^ /usr/include/c++/4.6/bits/stl_iterator.h:297:5: note: candidate template ignored: failed template argument deduction operator!=(const reverse_iterator<_Iterator>& __x, ^ /usr/include/c++/4.6/bits/stl_iterator.h:347:5: note: candidate template ignored: failed template argument deduction operator!=(const reverse_iterator<_IteratorL>& __x, ^ /usr/include/c++/4.6/bits/stl_iterator.h:811:5: note: candidate template ignored: failed template argument deduction operator!=(const __normal_iterator<_IteratorL, _Container>& __lhs, ^ /usr/include/c++/4.6/bits/stl_iterator.h:817:5: note: candidate template ignored: failed template argument deduction operator!=(const __normal_iterator<_Iterator, _Container>& __lhs, ^ /usr/include/c++/4.6/ext/new_allocator.h:128:5: note: candidate template ignored: failed template argument deduction operator!=(const new_allocator<_Tp>&, const new_allocator<_Tp>&) ^ /usr/include/c++/4.6/bits/allocator.h:132:5: note: candidate template ignored: failed template argument deduction operator!=(const allocator<_T1>&, const allocator<_T2>&) ^ /usr/include/c++/4.6/bits/allocator.h:137:5: note: candidate template ignored: failed template argument deduction operator!=(const allocator<_Tp>&, const allocator<_Tp>&) ^ /usr/include/c++/4.6/bits/basic_string.h:2472:5: note: candidate template ignored: failed template argument deduction operator!=(const basic_string<_CharT, _Traits, _Alloc>& __lhs, ^ /usr/include/c++/4.6/bits/basic_string.h:2484:5: note: candidate template ignored: failed template argument deduction operator!=(const _CharT* __lhs, ^ /usr/include/c++/4.6/bits/basic_string.h:2496:5: note: candidate template ignored: failed template argument deduction operator!=(const basic_string<_CharT, _Traits, _Alloc>& __lhs, ^ /usr/include/c++/4.6/bits/streambuf_iterator.h:199:5: note: candidate template ignored: failed template argument deduction operator!=(const istreambuf_iterator<_CharT, _Traits>& __a, ^ /usr/include/c++/4.6/bits/stl_vector.h:1297:5: note: candidate template ignored: failed template argument deduction operator!=(const vector<_Tp, _Alloc>& __x, const vector<_Tp, _Alloc>& __y) ^ /usr/include/c++/4.6/bits/stl_tree.h:315:5: note: candidate template ignored: failed template argument deduction operator!=(const _Rb_tree_iterator<_Val>& __x, ^ /usr/include/c++/4.6/bits/stl_tree.h:876:5: note: candidate template ignored: failed template argument deduction operator!=(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_set.h:720:5: note: candidate template ignored: failed template argument deduction operator!=(const set<_Key, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_multiset.h:703:5: note: candidate template ignored: failed template argument deduction operator!=(const multiset<_Key, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_map.h:906:5: note: candidate template ignored: failed template argument deduction operator!=(const map<_Key, _Tp, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_multimap.h:824:5: note: candidate template ignored: failed template argument deduction operator!=(const multimap<_Key, _Tp, _Compare, _Alloc>& __x, ^ sets.cpp:774:5: error: indirection requires pointer operand ('int' invalid) (*i)->missing = (*i)->flag; ^~ sets.cpp:774:21: error: indirection requires pointer operand ('int' invalid) (*i)->missing = (*i)->flag; ^~ mh.cpp:1312:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 4 errors generated. make[1]: *** [sets.o] Error 1 make[1]: *** Waiting for unfinished jobs.... 1 warning generated. 12 warnings generated. 3 warnings generated. 1 warning generated. 8 warnings generated. 1 warning generated. make[1]: Leaving directory `/build/plink-FKyQ9t/plink-1.07' make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0058 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-39b066c2-f17d-49a2-8ab6-1016e5a94b23/build/plink-FKyQ9t Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 37144 Build-Time: 13 Distribution: lsid64b Fail-Stage: build Install-Time: 7 Job: plink_1.07-1 Package: plink Package-Time: 32 Source-Version: 1.07-1 Space: 37144 Status: attempted Version: 1.07-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0058 Build needed 00:00:32, 37144k disc space DC-Message: Failed, but took only 153.546674. Retrying, you never know. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-26.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ plink 1.07-1 (amd64) 13 Jan 2012 01:05 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: plink Version: 1.07-1 Source Version: 1.07-1 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 4s (4215 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'plink' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/ Need to get 584 kB of source archives. Get:1 http://localhost/debian/ sid/main plink 1.07-1 (dsc) [1304 B] Get:2 http://localhost/debian/ sid/main plink 1.07-1 (tar) [577 kB] Get:3 http://localhost/debian/ sid/main plink 1.07-1 (diff) [5596 B] Fetched 584 kB in 0s (24.7 MB/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 `/build/plink-ZBlCZj/resolver-JKYqAC/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 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 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) ... Cannot open /var/lib/schroot/mount/lsid64b-02c8c872-cd2f-4ed4-885c-2a3ff06a5996/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), quilt, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), quilt, zlib1g-dev dpkg-deb: building package `sbuild-build-depends-plink-dummy' in `/build/plink-ZBlCZj/resolver-y2RHut/apt_archive/sbuild-build-depends-plink-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install plink 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 diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent 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 diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-plink-dummy zlib1g-dev 0 upgraded, 21 newly installed, 0 to remove and 10 not upgraded. Need to get 10.1 MB/10.1 MB of archives. After this operation, 27.3 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 libglib2.0-0 libxml2 libcroco3 libunistring0 bsdmainutils groff-base man-db libmagic1 file gettext-base html2text gettext intltool-debian po-debconf debhelper diffstat quilt zlib1g-dev sbuild-build-depends-plink-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:4 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:5 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:6 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:7 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:8 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:9 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:10 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:11 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:12 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:13 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:15 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:18 http://localhost/debian/ sid/main diffstat amd64 1.55-2 [29.9 kB] Get:19 http://localhost/debian/ sid/main quilt all 0.50-2 [381 kB] Get:20 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Preconfiguring packages ... Fetched 10.1 MB in 0s (41.7 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.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_8.9.14_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-2_amd64.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ... Selecting previously unselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-plink-dummy. Unpacking sbuild-build-depends-plink-dummy (from .../sbuild-build-depends-plink-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libpcre3 (8.12-4) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up bsdmainutils (8.2.3) ... 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 (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up diffstat (1.55-2) ... Setting up quilt (0.50-2) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ... Setting up sbuild-build-depends-plink-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 clang_3.0-5 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 libllvm3.0_3.0-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 quilt_0.50-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-plink-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Oct 23 14:33:43 2009 CEST using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./plink_1.07-1.dsc dpkg-source: info: extracting plink in plink-1.07 dpkg-source: info: unpacking plink_1.07.orig.tar.gz dpkg-source: info: applying plink_1.07-1.diff.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package plink dpkg-buildpackage: source version 1.07-1 dpkg-source --before-build plink-1.07 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean QUILT_PATCHES=debian/patches \ quilt --quiltrc /dev/null pop -a -R || test $? = 2 No patch removed rm -rf .pc debian/stamp-patched dh_testdir dh_testroot /usr/bin/make clean make[1]: Entering directory `/build/plink-ZBlCZj/plink-1.07' rm -f *.o *~ make[1]: Leaving directory `/build/plink-ZBlCZj/plink-1.07' dh_clean build-stamp install-stamp plink dpkg-source -b plink-1.07 dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1) dpkg-source: info: using source format `1.0' dpkg-source: info: building plink using existing plink_1.07.orig.tar.gz dpkg-source: info: building plink in plink_1.07-1.diff.gz dpkg-source: warning: ignoring deletion of file blox.cpp~ dpkg-source: warning: ignoring deletion of file webcheck.cpp~ dpkg-source: info: building plink in plink_1.07-1.dsc debian/rules build /usr/bin/make CXXFLAGS='-Wall -g -O2 -DWITH_R_PLUGINS -DUNIX' FORCE_DYNAMIC=1 QUILT_PATCHES=debian/patches \ quilt --quiltrc /dev/null push -a || test $? = 2 make[1]: Entering directory `/build/plink-ZBlCZj/plink-1.07' g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c plink.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c options.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c input.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c binput.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tinput.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genome.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c helper.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c stats.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c filters.cpp Applying patch 30_endiandetection.patch patching file Rsrv.h Hunk #1 succeeded at 321 (offset 8 lines). Now at patch 30_endiandetection.patch touch debian/stamp-patched g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c locus.cpp filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] int nm; ^ filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] double freq; ^ genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] int geno_nm = 0; ^ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] double tothet = 0; ^ stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteSNPs(del); ^ stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^ helper.cpp:219:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:232:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:244:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:256:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] double e10 = E10*S; ^ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] double e20 = E20*S; ^ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] double e21 = E21*S; ^ genome.cpp:1067:23: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~^~~~~~~~ ~~ genome.cpp:1067:23: note: place parentheses around the '&&' expression to silence this warning if ( (!par::silent ) && c==c2 || c==np) ^ ( ) helper.cpp:380:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:393:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ helper.cpp:407:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] int win_end = win_start + par::prune_ld_win; ^ filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] int x = 0; ^ plink.cpp:763:26: warning: '&&' within '||' [-Wlogical-op-parentheses] par::make_founders && ~~~~~~~~~~~~~~~~~~~^~ plink.cpp:763:26: note: place parentheses around the '&&' expression to silence this warning par::make_founders && ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c multi.cpp input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] bool success = false; ^ helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] set * s; ^ helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] int last = -1; ^ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] int thisChromosome = P.locus[0]->chr; ^ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] int nextChromosome; ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c crandom.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cluster.cpp multi.cpp:154:8: warning: unused variable 'is0zero' [-Wunused-variable] bool is0zero = IBDg.z0 < EPS ? true : false; ^ multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] bool is1zero = IBDg.z1 < EPS ? true : false; ^ cluster.cpp:492:8: warning: unused variable 'size' [-Wunused-variable] int size = peeps.size(); ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mds.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c output.cpp 4 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c informative.cpp mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] bool flag = svd(D,eigenvalue,eigenvector); ^ 8 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c assoc.cpp output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] int n_removed = deleteIndividuals(del); ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c epi.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c prephap.cpp assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^ 4 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c phase.cpp epi.cpp:438:12: warning: unused variable 'zero' [-Wunused-variable] double zero = 0; ^ epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] int c=0; ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c trio.cpp trio.cpp:252:26: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if ( mf->kid.size()>=0) ~~~~~~~~~~~~~~^ ~ trio.cpp:931:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteSNPs(mendel_locus); ^ trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteIndividuals(indel); ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tdt.cpp tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sharing.cpp 1 warning generated. 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genepi.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sets.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c perm.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mh.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genedrop.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c gxe.cpp genepi.cpp:78:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ genepi.cpp:169:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ genepi.cpp:506:10: warning: unused variable 'n12' [-Wunused-variable] int n12 = n1 + n2; ^ genepi.cpp:507:10: warning: unused variable 'ne' [-Wunused-variable] int ne = n1 < n2 ? n1 : n2; ^ sets.cpp:771:37: error: redefinition of 'i' with a different type vector::iterator i = PP->sample.begin(); ^ sets.cpp:703:12: note: previous definition is here for (int i=0; i > >')) while ( i != PP->sample.end() ) ~ ^ ~~~~~~~~~~~~~~~~ /usr/include/c++/4.6/bits/postypes.h:222:5: note: candidate template ignored: failed template argument deduction operator!=(const fpos<_StateT>& __lhs, const fpos<_StateT>& __rhs) ^ /usr/include/c++/4.6/bits/stl_pair.h:214:5: note: candidate template ignored: failed template argument deduction operator!=(const pair<_T1, _T2>& __x, const pair<_T1, _T2>& __y) ^ /usr/include/c++/4.6/bits/stl_iterator.h:297:5: note: candidate template ignored: failed template argument deduction operator!=(const reverse_iterator<_Iterator>& __x, ^ /usr/include/c++/4.6/bits/stl_iterator.h:347:5: note: candidate template ignored: failed template argument deduction operator!=(const reverse_iterator<_IteratorL>& __x, ^ /usr/include/c++/4.6/bits/stl_iterator.h:811:5: note: candidate template ignored: failed template argument deduction operator!=(const __normal_iterator<_IteratorL, _Container>& __lhs, ^ /usr/include/c++/4.6/bits/stl_iterator.h:817:5: note: candidate template ignored: failed template argument deduction operator!=(const __normal_iterator<_Iterator, _Container>& __lhs, ^ /usr/include/c++/4.6/ext/new_allocator.h:128:5: note: candidate template ignored: failed template argument deduction operator!=(const new_allocator<_Tp>&, const new_allocator<_Tp>&) ^ /usr/include/c++/4.6/bits/allocator.h:132:5: note: candidate template ignored: failed template argument deduction operator!=(const allocator<_T1>&, const allocator<_T2>&) ^ /usr/include/c++/4.6/bits/allocator.h:137:5: note: candidate template ignored: failed template argument deduction operator!=(const allocator<_Tp>&, const allocator<_Tp>&) ^ /usr/include/c++/4.6/bits/basic_string.h:2472:5: note: candidate template ignored: failed template argument deduction operator!=(const basic_string<_CharT, _Traits, _Alloc>& __lhs, ^ /usr/include/c++/4.6/bits/basic_string.h:2484:5: note: candidate template ignored: failed template argument deduction operator!=(const _CharT* __lhs, ^ /usr/include/c++/4.6/bits/basic_string.h:2496:5: note: candidate template ignored: failed template argument deduction operator!=(const basic_string<_CharT, _Traits, _Alloc>& __lhs, ^ /usr/include/c++/4.6/bits/streambuf_iterator.h:199:5: note: candidate template ignored: failed template argument deduction operator!=(const istreambuf_iterator<_CharT, _Traits>& __a, ^ /usr/include/c++/4.6/bits/stl_vector.h:1297:5: note: candidate template ignored: failed template argument deduction operator!=(const vector<_Tp, _Alloc>& __x, const vector<_Tp, _Alloc>& __y) ^ /usr/include/c++/4.6/bits/stl_tree.h:315:5: note: candidate template ignored: failed template argument deduction operator!=(const _Rb_tree_iterator<_Val>& __x, ^ /usr/include/c++/4.6/bits/stl_tree.h:876:5: note: candidate template ignored: failed template argument deduction operator!=(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_set.h:720:5: note: candidate template ignored: failed template argument deduction operator!=(const set<_Key, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_multiset.h:703:5: note: candidate template ignored: failed template argument deduction operator!=(const multiset<_Key, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_map.h:906:5: note: candidate template ignored: failed template argument deduction operator!=(const map<_Key, _Tp, _Compare, _Alloc>& __x, ^ /usr/include/c++/4.6/bits/stl_multimap.h:824:5: note: candidate template ignored: failed template argument deduction operator!=(const multimap<_Key, _Tp, _Compare, _Alloc>& __x, ^ sets.cpp:774:5: error: indirection requires pointer operand ('int' invalid) (*i)->missing = (*i)->flag; ^~ sets.cpp:774:21: error: indirection requires pointer operand ('int' invalid) (*i)->missing = (*i)->flag; ^~ genepi.cpp:1043:10: warning: unused variable 'n12' [-Wunused-variable] int n12 = n1 + n2; ^ genepi.cpp:1044:10: warning: unused variable 'ne' [-Wunused-variable] int ne = n1 < n2 ? n1 : n2;// ne = min(p,q) ^ genepi.cpp:1064:10: warning: unused variable 'nind' [-Wunused-variable] int nind = calcGENEPIMeanVariance(pSNP, ^ genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] bool casewise_deletion = false; ^ mh.cpp:1312:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 4 errors generated. make[1]: *** [sets.o] Error 1 make[1]: *** Waiting for unfinished jobs.... 1 warning generated. 12 warnings generated. 3 warnings generated. 1 warning generated. 1 warning generated. 8 warnings generated. make[1]: Leaving directory `/build/plink-ZBlCZj/plink-1.07' make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0106 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-02c8c872-cd2f-4ed4-885c-2a3ff06a5996/build/plink-ZBlCZj Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 37144 Build-Time: 12 Distribution: lsid64b Fail-Stage: build Install-Time: 6 Job: plink_1.07-1 Package: plink Package-Time: 31 Source-Version: 1.07-1 Space: 37144 Status: attempted Version: 1.07-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0106 Build needed 00:00:31, 37144k disc space DC-Build-Status: Failed 576.318812s ### Content of /var/log/daemon.log ### Jan 12 21:02:54 stremi-26 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Jan 12 21:04:00 stremi-26 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:14 stremi-26 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:29 stremi-26 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Jan 12 21:04:32 stremi-26 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:54 stremi-26 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Jan 12 21:05:17 stremi-26 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Jan 12 21:05:39 stremi-26 approx: Concurrent download of debian/dists/sid/Release is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 576.318812 versus expected 78 (r/m: 6.38870271794872 ; m: 78.0) DC-Build-Network: USED. See /tmp/rulesafter.AKcO4e ! ************************************************************ # Generated by iptables-save v1.4.8 on Fri Jan 13 01:06:03 2012 *filter :INPUT ACCEPT [3813496:28258817264] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [2025274:24294402843] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [370863:142237197] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT [29525:3934170] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [99:5940] -A OUTPUT -j LD [99:5940] -A LD -j LOG [99:5940] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Fri Jan 13 01:06:03 2012 ************************************************************ --- /tmp/rulesbefore.nRRImk 2012-01-13 00:56:26.925321131 +0100 +++ /tmp/rulesafter.AKcO4e 2012-01-13 01:06:03.253160857 +0100 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Fri Jan 13 00:56:26 2012 +# Generated by iptables-save v1.4.8 on Fri Jan 13 01:06:03 2012 *filter -:INPUT ACCEPT [3481377:24697591452] +:INPUT ACCEPT [3813496:28258817264] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[1772744:20941341094] -A OUTPUT -o lo -j ACCEPT +[2025274:24294402843] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,11 +16,11 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[348710:131635092] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[370863:142237197] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT -[28333:3778438] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[29525:3934170] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [99:5940] -A OUTPUT -j LD [99:5940] -A LD -j LOG [99:5940] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Fri Jan 13 00:56:26 2012 +# Completed on Fri Jan 13 01:06:03 2012 ************************************************************ [ 7937.778553] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=23173 DF PROTO=TCP SPT=43107 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7939.827842] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=9141 DF PROTO=TCP SPT=52461 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7941.993699] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=40105 DF PROTO=TCP SPT=58488 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7944.021578] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=10367 DF PROTO=TCP SPT=50233 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7955.716122] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=2828 DF PROTO=TCP SPT=33486 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7957.764026] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=45878 DF PROTO=TCP SPT=50571 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7959.897904] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=56074 DF PROTO=TCP SPT=55694 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7961.926179] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=35238 DF PROTO=TCP SPT=47163 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7972.421321] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=2351 DF PROTO=TCP SPT=33393 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7974.471649] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=997 DF PROTO=TCP SPT=34355 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7976.606109] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=53107 DF PROTO=TCP SPT=40309 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7978.633338] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=47011 DF PROTO=TCP SPT=37375 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7989.045487] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=29982 DF PROTO=TCP SPT=51512 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7991.092225] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=9229 DF PROTO=TCP SPT=37991 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7993.227089] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17401 DF PROTO=TCP SPT=45567 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7995.254128] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=4020 DF PROTO=TCP SPT=60541 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8006.186270] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=57946 DF PROTO=TCP SPT=37007 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8008.240437] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=59897 DF PROTO=TCP SPT=59671 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8010.406334] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=38058 DF PROTO=TCP SPT=36717 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8012.433798] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17352 DF PROTO=TCP SPT=37281 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8023.360375] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=13625 DF PROTO=TCP SPT=47773 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8025.409342] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=13737 DF PROTO=TCP SPT=50708 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8027.546835] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=42382 DF PROTO=TCP SPT=35611 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8029.573480] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=17846 DF PROTO=TCP SPT=41584 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8040.399611] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=18137 DF PROTO=TCP SPT=60384 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8042.448075] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=46205 DF PROTO=TCP SPT=35981 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8044.465301] graphmolMolOpsT[11527]: segfault at 0 ip 00002b1072ec7701 sp 00007fffaf058868 error 4 in libc-2.13.so[2b1072e4b000+17a000] [ 8044.615024] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=2482 DF PROTO=TCP SPT=37661 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8046.643226] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=58181 DF PROTO=TCP SPT=54563 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8057.772898] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=51272 DF PROTO=TCP SPT=59758 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8059.815857] IN= OUT=eth0 SRC=172.16.160.26 DST=63.246.24.167 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=40390 DF PROTO=TCP SPT=33983 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8061.951169] IN= OUT=eth0 SRC=172.16.160.26 DST=216.34.181.96 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=24508 DF PROTO=TCP SPT=38225 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8063.977660] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37998 DF PROTO=TCP SPT=35442 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 8101.673025] Disabling lock debugging due to kernel taint [ 8101.679027] Machine check events logged [ 8251.680052] Machine check events logged [ 8340.078333] lt-gstobject[29348]: segfault at 10 ip 00002b7ffe533540 sp 00007fff66674540 error 6 in libglib-2.0.so.0.3000.2[2b7ffe516000+f6000] [ 8776.672024] Machine check events logged [10726.677024] Machine check events logged [10876.676050] Machine check events logged [11701.672024] Machine check events logged [11851.673024] Machine check events logged [11926.681021] Machine check events logged [11964.185021] Machine check events logged [12025.137019] __ratelimit: 17 callbacks suppressed [12025.142238] Machine check events logged [12041.273017] Machine check events logged [12303.659380] IN= OUT=eth0 SRC=172.16.160.26 DST=24.24.24.24 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=42150 DF PROTO=TCP SPT=43583 DPT=9999 WINDOW=5840 RES=0x00 SYN URGP=0 [12303.676740] IN= OUT=eth0 SRC=172.16.160.26 DST=74.125.230.81 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=47705 DF PROTO=TCP SPT=41511 DPT=9999 WINDOW=5840 RES=0x00 SYN URGP=0 [13455.244768] IN= OUT=eth0 SRC=172.16.160.26 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=50664 DF PROTO=TCP SPT=37296 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 ************************************************************