DC-Build-Header: plink 1.07-1 / Sun Sep 11 13:06:00 +0200 2011 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 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 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 talc-120.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ plink 1.07-1 (amd64) 11 Sep 2011 13:11 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: plink Version: 1.07-1 Source Version: 1.07-1 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (61.2 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 (4030 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-q7dY2f/resolver-ZUD37Q/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 0 not upgraded. Need to get 0 B/698 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 deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 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/lsid64c-c99d9327-11e6-42f7-a9e4-51ba77a791c4/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-q7dY2f/resolver-OAYjb1/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 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 0 not upgraded. Need to get 9771 kB/9772 kB of archives. After this operation, 28.7 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3 libunistring0 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 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:4 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:5 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:6 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:7 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:8 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:9 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:10 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:11 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:12 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:13 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 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+nmu1 [223 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:18 http://localhost/debian/ sid/main diffstat amd64 1.54-1 [29.0 kB] Get:19 http://localhost/debian/ sid/main quilt all 0.48-7 [354 kB] Get:20 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Preconfiguring packages ... Fetched 9771 kB in 0s (60.8 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_5.08-1_amd64.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package diffstat. Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ... Selecting previously deselected package quilt. Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ... Selecting previously deselected 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 (1.2.0-3) ... Setting up libpcre3 (8.12-4) ... 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 (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up diffstat (1.54-1) ... Setting up quilt (0.48-7) ... 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_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 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-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): 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-q7dY2f/plink-1.07' rm -f *.o *~ make[1]: Leaving directory `/build/plink-q7dY2f/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-q7dY2f/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 In file included from input.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from input.cpp:13: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from plink.cpp:27: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from plink.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from locus.cpp:15: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from locus.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from options.cpp:16: In file included from ./options.h:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from options.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from genome.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from genome.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from tinput.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from tinput.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from filters.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from filters.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from binput.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from binput.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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; ^ In file included from stats.cpp:24: In file included from ./stats.h:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from stats.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] double freq; ^ filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] int nm; ^ In file included from helper.cpp:24: In file included from ./helper.h:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from helper.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^ 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:1067:32: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~~~~~~~~~ ^ genome.cpp:1067:32: note: place parentheses around the '&&' expression to silence this warning if ( (!par::silent ) && c==c2 || c==np) ^ ( ) input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] bool success = false; ^ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] int win_end = win_start + par::prune_ld_win; ^ filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteSNPs(del); ^ 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] } ^ stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ 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] } ^ plink.cpp:762:22: warning: '&&' within '||' [-Wlogical-op-parentheses] par::QTDT_test || ^ plink.cpp:762:22: note: place parentheses around the '&&' expression to silence this warning par::QTDT_test || ^ filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] int x = 0; ^ 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; ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c multi.cpp 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; ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c crandom.cpp In file included from multi.cpp:16: In file included from ./options.h:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from multi.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cluster.cpp multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] bool is1zero = IBDg.z1 < EPS ? true : false; ^ multi.cpp:154:8: warning: unused variable 'is0zero' [-Wunused-variable] bool is0zero = IBDg.z0 < EPS ? true : false; ^ In file included from cluster.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from cluster.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ cluster.cpp:492:8: warning: unused variable 'size' [-Wunused-variable] int size = peeps.size(); ^ 3 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mds.cpp In file included from mds.cpp:20: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from mds.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] bool flag = svd(D,eigenvalue,eigenvector); ^ 1 warning generated. 9 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c output.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c informative.cpp 5 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c assoc.cpp In file included from informative.cpp:17: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from informative.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from output.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from output.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c epi.cpp In file included from assoc.cpp:21: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from assoc.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] int n_removed = deleteIndividuals(del); ^ assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^ In file included from epi.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from epi.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c prephap.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; ^ In file included from prephap.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from prephap.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 3 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c phase.cpp In file included from phase.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from phase.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from phase.cpp:27: ./genogroup.h:42:14: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] template<> class less { ^~~~~ struct In file included from phase.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c trio.cpp In file included from trio.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from trio.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ trio.cpp:252:26: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if ( mf->kid.size()>=0) ~~~~~~~~~~~~~~^ ~ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tdt.cpp 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); ^ In file included from tdt.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from tdt.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^ 13 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sharing.cpp 2 warnings generated. In file included from sharing.cpp:18: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from sharing.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genepi.cpp 5 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sets.cpp In file included from genepi.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from genepi.cpp:16: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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; ^ 2 warnings generated. 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c perm.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mh.cpp In file included from sets.cpp:18: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from mh.cpp:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from mh.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from perm.cpp:17: In file included from ./perm.h:17: In file included from ./options.h:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from perm.cpp:13: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genedrop.cpp 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() ) ~ ^ ~~~~~~~~~~~~~~~~ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:38: In file included from /usr/include/c++/4.6/iosfwd:41: /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) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:40: In file included from /usr/include/c++/4.6/bits/char_traits.h:40: In file included from /usr/include/c++/4.6/bits/stl_algobase.h:65: /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) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:40: In file included from /usr/include/c++/4.6/bits/char_traits.h:40: In file included from /usr/include/c++/4.6/bits/stl_algobase.h:68: /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, ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:42: In file included from /usr/include/c++/4.6/bits/allocator.h:48: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/c++allocator.h:34: /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>&) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:42: /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>&) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:53: /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, ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:44: In file included from /usr/include/c++/4.6/bits/basic_ios.h:38: In file included from /usr/include/c++/4.6/bits/locale_facets.h:49: /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, ^ In file included from sets.cpp:18: In file included from ./plink.h:21: In file included from /usr/include/c++/4.6/vector:64: /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) ^ In file included from sets.cpp:18: In file included from ./plink.h:22: In file included from /usr/include/c++/4.6/set:59: /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:866:5: note: candidate template ignored: failed template argument deduction operator!=(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& __x, ^ In file included from sets.cpp:18: In file included from ./plink.h:22: In file included from /usr/include/c++/4.6/set:60: /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, ^ In file included from sets.cpp:18: In file included from ./plink.h:22: In file included from /usr/include/c++/4.6/set:61: /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, ^ In file included from sets.cpp:18: In file included from ./plink.h:23: In file included from /usr/include/c++/4.6/map:60: /usr/include/c++/4.6/bits/stl_map.h:901:5: note: candidate template ignored: failed template argument deduction operator!=(const map<_Key, _Tp, _Compare, _Alloc>& __x, ^ In file included from sets.cpp:18: In file included from ./plink.h:23: In file included from /usr/include/c++/4.6/map:61: /usr/include/c++/4.6/bits/stl_multimap.h:819:5: 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] } ^ In file included from genedrop.cpp:16: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from genedrop.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 1 warning and 4 errors generated. make[1]: *** [sets.o] Error 1 make[1]: *** Waiting for unfinished jobs.... 9 warnings generated. 1 warning generated. 1 warning generated. 1 warning generated. 2 warnings generated. 4 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. make: *** [build-stamp] Error 2 make[1]: Leaving directory `/build/plink-q7dY2f/plink-1.07' dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1312 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-c99d9327-11e6-42f7-a9e4-51ba77a791c4/build/plink-q7dY2f Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 22656 Build-Time: 60 Distribution: lsid64c Fail-Stage: build Install-Time: 4 Job: plink_1.07-1 Package: plink Package-Time: 76 Source-Version: 1.07-1 Space: 22656 Status: attempted Version: 1.07-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1312 Build needed 00:01:16, 22656k disc space DC-Message: Failed, but took only 377.068954. Retrying, you never know. 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 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 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 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 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 Requested exclusive mode, but other builds running. 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Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-120.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ plink 1.07-1 (amd64) 11 Sep 2011 13:31 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: plink Version: 1.07-1 Source Version: 1.07-1 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (64.1 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 (36.9 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-i0kYfs/resolver-d2wO93/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 0 not upgraded. Need to get 0 B/700 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 deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 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/lsid64c-d2d51bf1-87b0-44d9-89b0-cab40cdcc740/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-i0kYfs/resolver-wd7UqP/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 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 0 not upgraded. Need to get 9771 kB/9772 kB of archives. After this operation, 28.7 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3 libunistring0 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 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:4 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:5 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:6 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:7 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:8 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:9 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:10 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:11 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:12 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:13 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 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+nmu1 [223 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:18 http://localhost/debian/ sid/main diffstat amd64 1.54-1 [29.0 kB] Get:19 http://localhost/debian/ sid/main quilt all 0.48-7 [354 kB] Get:20 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Preconfiguring packages ... Fetched 9771 kB in 0s (61.3 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_5.08-1_amd64.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package diffstat. Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ... Selecting previously deselected package quilt. Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ... Selecting previously deselected 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 (1.2.0-3) ... Setting up libpcre3 (8.12-4) ... 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 (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up diffstat (1.54-1) ... Setting up quilt (0.48-7) ... 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_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 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-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 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: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): 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-i0kYfs/plink-1.07' rm -f *.o *~ make[1]: Leaving directory `/build/plink-i0kYfs/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-i0kYfs/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 In file included from options.cpp:16: In file included from ./options.h:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from options.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c locus.cpp In file included from genome.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from genome.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from binput.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from binput.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from helper.cpp:24: In file included from ./helper.h:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from helper.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from plink.cpp:27: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from plink.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from filters.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from filters.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from input.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from input.cpp:13: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] double freq; ^ filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] int nm; ^ 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; ^ In file included from tinput.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from tinput.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteSNPs(del); ^ 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] } ^ 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] } ^ In file included from stats.cpp:24: In file included from ./stats.h:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from stats.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] int x = 0; ^ plink.cpp:762:22: warning: '&&' within '||' [-Wlogical-op-parentheses] par::QTDT_test || ^ plink.cpp:762:22: note: place parentheses around the '&&' expression to silence this warning par::QTDT_test || ^ genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^ helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ In file included from locus.cpp:15: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from locus.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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:1067:32: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~~~~~~~~~ ^ genome.cpp:1067:32: note: place parentheses around the '&&' expression to silence this warning if ( (!par::silent ) && c==c2 || c==np) ^ ( ) 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; ^ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] int win_end = win_start + par::prune_ld_win; ^ input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] bool success = false; ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c multi.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c crandom.cpp In file included from multi.cpp:16: In file included from ./options.h:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from multi.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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; ^ In file included from cluster.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from cluster.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ cluster.cpp:492:8: warning: unused variable 'size' [-Wunused-variable] int size = peeps.size(); ^ 3 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mds.cpp 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c output.cpp In file included from mds.cpp:20: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from mds.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 5 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); ^ In file included from output.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from output.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 9 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c assoc.cpp In file included from informative.cpp:17: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from informative.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] int n_removed = deleteIndividuals(del); ^ In file included from assoc.cpp:21: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from assoc.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c epi.cpp In file included from epi.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from epi.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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; ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c prephap.cpp In file included from prephap.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from prephap.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 3 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c phase.cpp In file included from phase.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from phase.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from phase.cpp:27: ./genogroup.h:42:14: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] template<> class less { ^~~~~ struct In file included from phase.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c trio.cpp 13 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tdt.cpp In file included from trio.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from trio.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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); ^ In file included from tdt.cpp:22: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from tdt.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 5 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sharing.cpp 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genepi.cpp tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^ In file included from sharing.cpp:18: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from sharing.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ In file included from genepi.cpp:23: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from genepi.cpp:16: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 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; ^ 1 warning generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sets.cpp In file included from sets.cpp:18: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c perm.cpp 2 warnings generated. g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mh.cpp 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() ) ~ ^ ~~~~~~~~~~~~~~~~ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:38: In file included from /usr/include/c++/4.6/iosfwd:41: /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) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:40: In file included from /usr/include/c++/4.6/bits/char_traits.h:40: In file included from /usr/include/c++/4.6/bits/stl_algobase.h:65: /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) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:40: In file included from /usr/include/c++/4.6/bits/char_traits.h:40: In file included from /usr/include/c++/4.6/bits/stl_algobase.h:68: /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, ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:42: In file included from /usr/include/c++/4.6/bits/allocator.h:48: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/c++allocator.h:34: /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>&) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:42: /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>&) ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:53: /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, ^ In file included from sets.cpp:15: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:44: In file included from /usr/include/c++/4.6/bits/basic_ios.h:38: In file included from /usr/include/c++/4.6/bits/locale_facets.h:49: /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, ^ In file included from sets.cpp:18: In file included from ./plink.h:21: In file included from /usr/include/c++/4.6/vector:64: /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) ^ In file included from sets.cpp:18: In file included from ./plink.h:22: In file included from /usr/include/c++/4.6/set:59: /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:866:5: note: candidate template ignored: failed template argument deduction operator!=(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& __x, ^ In file included from sets.cpp:18: In file included from ./plink.h:22: In file included from /usr/include/c++/4.6/set:60: /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, ^ In file included from sets.cpp:18: In file included from ./plink.h:22: In file included from /usr/include/c++/4.6/set:61: /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, ^ In file included from sets.cpp:18: In file included from ./plink.h:23: In file included from /usr/include/c++/4.6/map:60: /usr/include/c++/4.6/bits/stl_map.h:901:5: note: candidate template ignored: failed template argument deduction operator!=(const map<_Key, _Tp, _Compare, _Alloc>& __x, ^ In file included from sets.cpp:18: In file included from ./plink.h:23: In file included from /usr/include/c++/4.6/map:61: /usr/include/c++/4.6/bits/stl_multimap.h:819:5: 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; ^~ In file included from perm.cpp:17: In file included from ./perm.h:17: In file included from ./options.h:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from perm.cpp:13: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ 1 warning and 4 errors generated. make[1]: *** [sets.o] Error 1 make[1]: *** Waiting for unfinished jobs.... In file included from mh.cpp:19: ./plink.h:388:5: warning: class template 'less' was previously declared as a struct template [-Wmismatched-tags] class less { ^~~~~ struct In file included from mh.cpp:14: In file included from /usr/include/c++/4.6/iostream:39: In file included from /usr/include/c++/4.6/ostream:39: In file included from /usr/include/c++/4.6/ios:42: In file included from /usr/include/c++/4.6/bits/ios_base.h:42: In file included from /usr/include/c++/4.6/bits/locale_classes.h:41: In file included from /usr/include/c++/4.6/string:49: /usr/include/c++/4.6/bits/stl_function.h:232:12: note: previous use is here struct less : public binary_function<_Tp, _Tp, bool> ^ mh.cpp:1312:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 2 warnings generated. 1 warning generated. 9 warnings generated. 2 warnings generated. 1 warning generated. 4 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. make[1]: Leaving directory `/build/plink-i0kYfs/plink-1.07' make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1332 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-d2d51bf1-87b0-44d9-89b0-cab40cdcc740/build/plink-i0kYfs Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 22096 Build-Time: 48 Distribution: lsid64c Fail-Stage: build Install-Time: 4 Job: plink_1.07-1 Package: plink Package-Time: 63 Source-Version: 1.07-1 Space: 22096 Status: attempted Version: 1.07-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1332 Build needed 00:01:03, 22096k disc space DC-Build-Status: Failed 1611.693032s ### Content of /var/log/daemon.log ### Sep 11 10:47:38 talc-120 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:47:49 talc-120 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:00 talc-120 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:15 talc-120 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:31 talc-120 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:48:33 talc-120 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:48:42 talc-120 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:48:56 talc-120 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:07 talc-120 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:07 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:25 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:25 talc-120 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:44 talc-120 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:48 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:55 talc-120 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:59 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:10 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:21 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:45 talc-120 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 1611.693032 versus expected 168 (r/m: 8.5934109047619 ; m: 168.0) DC-Build-Network: USED. See /tmp/rulesafter.m9Zxny ! ************************************************************ # Generated by iptables-save v1.4.8 on Sun Sep 11 13:32:52 2011 *filter :INPUT ACCEPT [3638153:19315506766] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [1327609:16848708257] -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 [788790:130950225] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [5343:513720] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [5:280] -A OUTPUT -j LD [5:280] -A LD -j LOG [5:280] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Sun Sep 11 13:32:52 2011 ************************************************************ --- /tmp/rulesbefore.TzGeuA 2011-09-11 13:06:00.411645155 +0200 +++ /tmp/rulesafter.m9Zxny 2011-09-11 13:32:52.111646168 +0200 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Sun Sep 11 13:06:00 2011 +# Generated by iptables-save v1.4.8 on Sun Sep 11 13:32:52 2011 *filter -:INPUT ACCEPT [3200233:16937617852] +:INPUT ACCEPT [3638153:19315506766] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[1161477:14721393179] -A OUTPUT -o lo -j ACCEPT +[1327609:16848708257] -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 @@ -16,10 +16,10 @@ [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 -[706932:104931529] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT -[4514:435380] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT -[3:160] -A OUTPUT -j LD -[3:160] -A LD -j LOG -[3:160] -A LD -j REJECT --reject-with icmp-port-unreachable +[788790:130950225] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[5343:513720] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[5:280] -A OUTPUT -j LD +[5:280] -A LD -j LOG +[5:280] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Sun Sep 11 13:06:00 2011 +# Completed on Sun Sep 11 13:32:52 2011 ************************************************************ [ 11.742161] alloc irq_desc for 56 on node -1 [ 11.742163] alloc kstat_irqs on node -1 [ 11.742171] ioatdma 0000:00:0f.0: irq 56 for MSI/MSI-X [ 11.742173] alloc irq_desc for 57 on node -1 [ 11.742175] alloc kstat_irqs on node -1 [ 11.742178] ioatdma 0000:00:0f.0: irq 57 for MSI/MSI-X [ 11.742180] alloc irq_desc for 58 on node -1 [ 11.742181] alloc kstat_irqs on node -1 [ 11.742185] ioatdma 0000:00:0f.0: irq 58 for MSI/MSI-X [ 11.742186] alloc irq_desc for 59 on node -1 [ 11.742188] alloc kstat_irqs on node -1 [ 11.742191] ioatdma 0000:00:0f.0: irq 59 for MSI/MSI-X [ 11.793753] EDAC MC: Ver: 2.1.0 Mar 7 2011 [ 11.819541] intel_rng: FWH not detected [ 12.042419] EDAC MC0: Giving out device to 'i5400_edac.c' 'I5400': DEV 0000:00:10.0 [ 12.088399] EDAC PCI0: Giving out device to module 'i5400_edac' controller 'EDAC PCI controller': DEV '0000:00:10.0' (POLLED) [ 12.096923] Error: Driver 'pcspkr' is already registered, aborting... [ 12.340616] Adding 3911788k swap on /dev/sda1. Priority:-1 extents:1 across:3911788k [ 12.390304] EXT3 FS on sda3, internal journal [ 12.634772] kjournald starting. Commit interval 5 seconds [ 12.634778] EXT3-fs warning: maximal mount count reached, running e2fsck is recommended [ 12.634923] EXT3 FS on sda5, internal journal [ 12.634928] EXT3-fs: mounted filesystem with ordered data mode. [ 13.057752] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.112049] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.114179] ADDRCONF(NETDEV_UP): eth0: link is not ready [ 16.223933] e1000e: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX/TX [ 16.273665] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready [ 26.496005] eth0: no IPv6 routers present [ 293.935148] RPC: Registered udp transport module. [ 293.963389] RPC: Registered tcp transport module. [ 293.991617] RPC: Registered tcp NFSv4.1 backchannel transport module. [ 294.052952] Slow work thread pool: Starting up [ 294.079740] Slow work thread pool: Ready [ 294.103362] FS-Cache: Loaded [ 294.150825] FS-Cache: Netfs 'nfs' registered for caching [ 294.186609] svc: failed to register lockdv1 RPC service (errno 97). [ 322.165509] Adding 296929352k swap on /dev/sda5. Priority:-2 extents:1 across:296929352k [ 337.135761] ip_tables: (C) 2000-2006 Netfilter Core Team [ 341.508015] IN= OUT=eth0 SRC=172.16.66.120 DST=224.0.0.22 LEN=40 TOS=0x00 PREC=0xC0 TTL=1 ID=0 DF PROTO=2 [ 1061.120359] cpp[25552]: segfault at 0 ip 000000000057b5ef sp 00007fffa9422fa0 error 4 in clang[400000+8e1000] [ 3816.680626] cpp[11811]: segfault at 0 ip 000000000057b5ef sp 00007fff81a0eab0 error 4 in clang[400000+8e1000] [ 4049.627547] cpp[23720]: segfault at 0 ip 000000000057b5ef sp 00007fffe697b540 error 4 in clang[400000+8e1000] [ 4520.384979] IN= OUT=eth0 SRC=172.16.66.120 DST=192.0.32.8 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=33762 DF PROTO=TCP SPT=57924 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 4523.468019] IN= OUT=eth0 SRC=172.16.66.120 DST=192.0.32.8 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=33763 DF PROTO=TCP SPT=57924 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 5268.458814] cpp[9186]: segfault at 0 ip 000000000057b5ef sp 00007fffb62f6ab0 error 4 in clang[400000+8e1000] [ 6022.373606] clang[24836]: segfault at 8 ip 0000000000803627 sp 00007fffb2876d00 error 4 in clang[400000+8e1000] [ 6220.064923] clang[28300]: segfault at 8 ip 0000000000803627 sp 00007ffffc0e3910 error 4 in clang[400000+8e1000] [10130.552673] IN= OUT=eth0 SRC=172.16.66.120 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=34148 DF PROTO=TCP SPT=43642 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [10133.648019] IN= OUT=eth0 SRC=172.16.66.120 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=34149 DF PROTO=TCP SPT=43642 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 ************************************************************