RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '9602b7344ff832c1eaf59509a0bed6aa938678f3', '/home/buildd/filecache-default/3df3a59274f4bcdc3d138197d23a7243c9362cee'] Synching the system clock with the buildd NTP service... 1 Dec 08:35:50 ntpdate[12323]: adjust time server 10.211.37.1 offset -0.000616 sec Unpacking chroot for build 9602b7344ff832c1eaf59509a0bed6aa938678f3 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '9602b7344ff832c1eaf59509a0bed6aa938678f3'] Mounting chroot for build 9602b7344ff832c1eaf59509a0bed6aa938678f3 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '9602b7344ff832c1eaf59509a0bed6aa938678f3', 'deb http://ftpmaster.internal/ubuntu precise main universe'] Overriding sources.list in build-9602b7344ff832c1eaf59509a0bed6aa938678f3 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '9602b7344ff832c1eaf59509a0bed6aa938678f3', 'armhf'] Updating debian chroot for build 9602b7344ff832c1eaf59509a0bed6aa938678f3 Ign http://archive-team.internal precise InRelease Ign http://archive-team.internal precise Release.gpg Get:1 http://archive-team.internal precise Release [463 B] Ign http://ftpmaster.internal precise InRelease Ign http://archive-team.internal precise/main TranslationIndex Get:2 http://ftpmaster.internal precise Release.gpg [198 B] Get:3 http://ftpmaster.internal precise Release [49.6 kB] Get:4 http://ftpmaster.internal precise/main armhf Packages [958 kB] Get:5 http://archive-team.internal precise/main armhf Packages [1642 kB] Get:6 http://ftpmaster.internal precise/universe armhf Packages [2240 kB] Ign http://archive-team.internal precise/main Translation-en Get:7 http://ftpmaster.internal precise/main TranslationIndex [3502 B] Get:8 http://ftpmaster.internal precise/universe TranslationIndex [2712 B] Get:9 http://ftpmaster.internal precise/main Translation-en [716 kB] Get:10 http://ftpmaster.internal precise/universe Translation-en [3293 kB] Fetched 8904 kB in 23s (377 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: advancecomp apt base-files binutils bsdutils coreutils cpio cpp diffutils dpkg e2fslibs findutils g++ gcc gnupg grep initramfs-tools-bin libacl1 libapt-pkg4.11 libattr1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libdbus-1-3 libffi6 libgdbm3 libglib2.0-0 libmount1 libmpc2 libnih1 libpam-modules libpcre3 libreadline6 libslang2 libssl1.0.0 libtinfo5 login make module-init-tools multiarch-support optipng passwd perl perl-base pkgbinarymangler procps python2.7-minimal sed sysvinit-utils tar udev upstart util-linux xz-utils 56 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 29.3 MB of archives. After this operation, 26.7 MB disk space will be freed. WARNING: The following packages cannot be authenticated! base-files upstart libc-dev-bin libc6-dev libc-bin libc6 libdbus-1-3 libnih1 sysvinit-utils libattr1 libacl1 dpkg coreutils diffutils findutils grep login libgdbm3 perl perl-base sed tar util-linux bsdutils libtinfo5 libreadline6 e2fslibs libblkid1 libmount1 libpam-modules libslang2 libssl1.0.0 libffi6 libpcre3 libglib2.0-0 module-init-tools libmpc2 libapt-pkg4.11 gnupg apt multiarch-support passwd python2.7-minimal xz-utils cpio initramfs-tools-bin procps udev advancecomp binutils cpp gcc g++ make optipng pkgbinarymangler Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main base-files armhf 6.5ubuntu3 [65.8 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main upstart armhf 1.3-0ubuntu11 [281 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libc-dev-bin armhf 2.13-20ubuntu6 [73.3 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libc6-dev armhf 2.13-20ubuntu6 [2214 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libc-bin armhf 2.13-20ubuntu6 [842 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libc6 armhf 2.13-20ubuntu6 [3832 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libdbus-1-3 armhf 1.4.16-1ubuntu1 [117 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main libnih1 armhf 1.0.3-4ubuntu5 [48.7 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main sysvinit-utils armhf 2.88dsf-13.10ubuntu5 [57.6 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main libattr1 armhf 1:2.4.46-3ubuntu1 [9430 B] Get:11 http://ftpmaster.internal/ubuntu/ precise/main libacl1 armhf 2.2.51-4ubuntu1 [14.6 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main dpkg armhf 1.16.1.2ubuntu1 [1755 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main coreutils armhf 8.13-3ubuntu2 [1941 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main diffutils armhf 1:3.2-1 [190 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main findutils armhf 4.4.2-1ubuntu3 [290 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main grep armhf 2.9-2 [216 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main login armhf 1:4.1.4.2+svn3283-3ubuntu2 [276 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main libgdbm3 armhf 1.8.3-10 [31.9 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main perl armhf 5.14.2-5ubuntu1 [3618 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main perl-base armhf 5.14.2-5ubuntu1 [1351 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main sed armhf 4.2.1-9 [134 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main tar armhf 1.26-3ubuntu1 [188 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main util-linux armhf 2.19.1-2ubuntu3 [537 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main bsdutils armhf 1:2.19.1-2ubuntu3 [32.4 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main libtinfo5 armhf 5.9-4 [80.8 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main libreadline6 armhf 6.2-8 [112 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main e2fslibs armhf 1.42~WIP-2011-10-16-1ubuntu1 [169 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libblkid1 armhf 2.19.1-2ubuntu3 [61.7 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main libmount1 armhf 2.19.1-2ubuntu3 [53.8 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libpam-modules armhf 1.1.3-6ubuntu1 [242 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libslang2 armhf 2.2.4-3ubuntu1 [426 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/main libssl1.0.0 armhf 1.0.0e-2ubuntu4 [782 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main libffi6 armhf 3.0.11~rc1-5 [16.7 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/main libpcre3 armhf 8.12-4 [143 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main libglib2.0-0 armhf 2.30.1-2ubuntu1 [992 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise/main module-init-tools armhf 3.16-1ubuntu2 [84.8 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise/main libmpc2 armhf 0.9-4 [31.0 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise/main libapt-pkg4.11 armhf 0.8.16~exp5ubuntu14.1 [450 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise/main gnupg armhf 1.4.11-3ubuntu2 [717 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise/main apt armhf 0.8.16~exp5ubuntu14.1 [1019 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise/main multiarch-support armhf 2.13-20ubuntu6 [4480 B] Get:42 http://ftpmaster.internal/ubuntu/ precise/main passwd armhf 1:4.1.4.2+svn3283-3ubuntu2 [791 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise/main python2.7-minimal armhf 2.7.2-5ubuntu1 [1484 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise/main xz-utils armhf 5.1.1alpha+20110809-3 [83.0 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main cpio armhf 2.11-7ubuntu1 [99.4 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main initramfs-tools-bin armhf 0.99ubuntu9 [11.3 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise/main procps armhf 1:3.2.8-11ubuntu4 [228 kB] Get:48 http://ftpmaster.internal/ubuntu/ precise/main udev armhf 175-0ubuntu2 [293 kB] Get:49 http://ftpmaster.internal/ubuntu/ precise/main advancecomp armhf 1.15-1 [260 kB] Get:50 http://ftpmaster.internal/ubuntu/ precise/main binutils armhf 2.22-1ubuntu1 [2260 kB] Get:51 http://ftpmaster.internal/ubuntu/ precise/main cpp armhf 4:4.6.1-2ubuntu5 [27.8 kB] Get:52 http://ftpmaster.internal/ubuntu/ precise/main gcc armhf 4:4.6.1-2ubuntu5 [5112 B] Get:53 http://ftpmaster.internal/ubuntu/ precise/main g++ armhf 4:4.6.1-2ubuntu5 [1452 B] Get:54 http://ftpmaster.internal/ubuntu/ precise/main make armhf 3.81-8.1ubuntu1 [103 kB] Get:55 http://ftpmaster.internal/ubuntu/ precise/main optipng armhf 0.6.4-1 [82.5 kB] Get:56 http://ftpmaster.internal/ubuntu/ precise/main pkgbinarymangler all 109 [28.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 29.3 MB in 7s (3835 kB/s) (Reading database ... 11561 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu2 (using .../base-files_6.5ubuntu3_armhf.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu3) ... (Reading database ... 11561 files and directories currently installed.) Preparing to replace upstart 1.3-0ubuntu11 (using .../upstart_1.3-0ubuntu11_armhf.deb) ... Unpacking replacement upstart ... Preparing to replace libc-dev-bin 2.13-20ubuntu5.1 (using .../libc-dev-bin_2.13-20ubuntu6_armhf.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.13-20ubuntu5.1 (using .../libc6-dev_2.13-20ubuntu6_armhf.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.13-20ubuntu5.1 (using .../libc-bin_2.13-20ubuntu6_armhf.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20ubuntu6) ... (Reading database ... 11556 files and directories currently installed.) Preparing to replace libc6 2.13-20ubuntu5.1 (using .../libc6_2.13-20ubuntu6_armhf.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20ubuntu6) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11555 files and directories currently installed.) Preparing to replace libdbus-1-3 1.4.16-1ubuntu1 (using .../libdbus-1-3_1.4.16-1ubuntu1_armhf.deb) ... Unpacking replacement libdbus-1-3 ... Preparing to replace libnih1 1.0.3-4ubuntu5 (using .../libnih1_1.0.3-4ubuntu5_armhf.deb) ... Unpacking replacement libnih1 ... Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu5 (using .../sysvinit-utils_2.88dsf-13.10ubuntu5_armhf.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace libattr1 1:2.4.46-3 (using .../libattr1_1%3a2.4.46-3ubuntu1_armhf.deb) ... Unpacking replacement libattr1 ... Setting up libattr1 (1:2.4.46-3ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11553 files and directories currently installed.) Preparing to replace libacl1 2.2.51-3 (using .../libacl1_2.2.51-4ubuntu1_armhf.deb) ... Unpacking replacement libacl1 ... Setting up libacl1 (2.2.51-4ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11552 files and directories currently installed.) Preparing to replace dpkg 1.16.1.2ubuntu1 (using .../dpkg_1.16.1.2ubuntu1_armhf.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.16.1.2ubuntu1) ... (Reading database ... 11551 files and directories currently installed.) Preparing to replace coreutils 8.13-3ubuntu1 (using .../coreutils_8.13-3ubuntu2_armhf.deb) ... Unpacking replacement coreutils ... Setting up coreutils (8.13-3ubuntu2) ... (Reading database ... 11509 files and directories currently installed.) Preparing to replace diffutils 1:3.2-1 (using .../diffutils_1%3a3.2-1_armhf.deb) ... Unpacking replacement diffutils ... Setting up diffutils (1:3.2-1) ... (Reading database ... 11476 files and directories currently installed.) Preparing to replace findutils 4.4.2-1ubuntu3 (using .../findutils_4.4.2-1ubuntu3_armhf.deb) ... Unpacking replacement findutils ... Setting up findutils (4.4.2-1ubuntu3) ... (Reading database ... 11434 files and directories currently installed.) Preparing to replace grep 2.9-2 (using .../archives/grep_2.9-2_armhf.deb) ... Unpacking replacement grep ... Setting up grep (2.9-2) ... (Reading database ... 11391 files and directories currently installed.) Preparing to replace login 1:4.1.4.2+svn3283-3ubuntu2 (using .../login_1%3a4.1.4.2+svn3283-3ubuntu2_armhf.deb) ... Unpacking replacement login ... Setting up login (1:4.1.4.2+svn3283-3ubuntu2) ... (Reading database ... 11347 files and directories currently installed.) Preparing to replace libgdbm3 1.8.3-10 (using .../libgdbm3_1.8.3-10_armhf.deb) ... Unpacking replacement libgdbm3 ... Preparing to replace perl 5.14.2-5 (using .../perl_5.14.2-5ubuntu1_armhf.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-5 (using .../perl-base_5.14.2-5ubuntu1_armhf.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-5ubuntu1) ... (Reading database ... 11346 files and directories currently installed.) Preparing to replace sed 4.2.1-9 (using .../archives/sed_4.2.1-9_armhf.deb) ... Unpacking replacement sed ... Setting up sed (4.2.1-9) ... (Reading database ... 11307 files and directories currently installed.) Preparing to replace tar 1.25-3 (using .../tar_1.26-3ubuntu1_armhf.deb) ... Unpacking replacement tar ... Setting up tar (1.26-3ubuntu1) ... (Reading database ... 11267 files and directories currently installed.) Preparing to replace util-linux 2.19.1-2ubuntu3 (using .../util-linux_2.19.1-2ubuntu3_armhf.deb) ... Unpacking replacement util-linux ... Setting up libdbus-1-3 (1.4.16-1ubuntu1) ... Setting up libnih1 (1.0.3-4ubuntu5) ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu5) ... Setting up upstart (1.3-0ubuntu11) ... Setting up util-linux (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11266 files and directories currently installed.) Preparing to replace bsdutils 1:2.19.1-2ubuntu3 (using .../bsdutils_1%3a2.19.1-2ubuntu3_armhf.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.19.1-2ubuntu3) ... (Reading database ... 11265 files and directories currently installed.) Preparing to replace libtinfo5 5.9-4 (using .../libtinfo5_5.9-4_armhf.deb) ... Unpacking replacement libtinfo5 ... Setting up libtinfo5 (5.9-4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11264 files and directories currently installed.) Preparing to replace libreadline6 6.2-2 (using .../libreadline6_6.2-8_armhf.deb) ... Unpacking replacement libreadline6 ... Setting up libreadline6 (6.2-8) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11263 files and directories currently installed.) Preparing to replace e2fslibs 1.42~WIP-2011-10-16-1ubuntu1 (using .../e2fslibs_1.42~WIP-2011-10-16-1ubuntu1_armhf.deb) ... Unpacking replacement e2fslibs ... Setting up e2fslibs (1.42~WIP-2011-10-16-1ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11263 files and directories currently installed.) Preparing to replace libblkid1 2.19.1-2ubuntu3 (using .../libblkid1_2.19.1-2ubuntu3_armhf.deb) ... Unpacking replacement libblkid1 ... Setting up libblkid1 (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11262 files and directories currently installed.) Preparing to replace libmount1 2.19.1-2ubuntu3 (using .../libmount1_2.19.1-2ubuntu3_armhf.deb) ... Unpacking replacement libmount1 ... Setting up libmount1 (2.19.1-2ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11261 files and directories currently installed.) Preparing to replace libpam-modules 1.1.3-6ubuntu1 (using .../libpam-modules_1.1.3-6ubuntu1_armhf.deb) ... Unpacking replacement libpam-modules ... Setting up libpam-modules (1.1.3-6ubuntu1) ... (Reading database ... 11261 files and directories currently installed.) Preparing to replace libslang2 2.2.4-3ubuntu1 (using .../libslang2_2.2.4-3ubuntu1_armhf.deb) ... Unpacking replacement libslang2 ... Setting up libslang2 (2.2.4-3ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11260 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.0e-2ubuntu4 (using .../libssl1.0.0_1.0.0e-2ubuntu4_armhf.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.0e-2ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11259 files and directories currently installed.) Preparing to replace libffi6 3.0.11~rc1-1 (using .../libffi6_3.0.11~rc1-5_armhf.deb) ... Unpacking replacement libffi6 ... Preparing to replace libpcre3 8.12-4 (using .../libpcre3_8.12-4_armhf.deb) ... Unpacking replacement libpcre3 ... Preparing to replace libglib2.0-0 2.30.1-2ubuntu1 (using .../libglib2.0-0_2.30.1-2ubuntu1_armhf.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace module-init-tools 3.16-1ubuntu1 (using .../module-init-tools_3.16-1ubuntu2_armhf.deb) ... Unpacking replacement module-init-tools ... Preparing to replace libmpc2 0.9-4 (using .../libmpc2_0.9-4_armhf.deb) ... Unpacking replacement libmpc2 ... Preparing to replace libapt-pkg4.11 0.8.16~exp5ubuntu14.1 (using .../libapt-pkg4.11_0.8.16~exp5ubuntu14.1_armhf.deb) ... Unpacking replacement libapt-pkg4.11 ... Setting up libapt-pkg4.11 (0.8.16~exp5ubuntu14.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 11210 files and directories currently installed.) Preparing to replace gnupg 1.4.11-3ubuntu2 (using .../gnupg_1.4.11-3ubuntu2_armhf.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.11-3ubuntu2) ... (Reading database ... 11168 files and directories currently installed.) Preparing to replace apt 0.8.16~exp5ubuntu14.1 (using .../apt_0.8.16~exp5ubuntu14.1_armhf.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp5ubuntu14.1) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: Total number processed: 2 gpg: unchanged: 2 (Reading database ... 11168 files and directories currently installed.) Preparing to replace multiarch-support 2.13-20ubuntu5.1 (using .../multiarch-support_2.13-20ubuntu6_armhf.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20ubuntu6) ... (Reading database ... 11167 files and directories currently installed.) Preparing to replace passwd 1:4.1.4.2+svn3283-3ubuntu2 (using .../passwd_1%3a4.1.4.2+svn3283-3ubuntu2_armhf.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.4.2+svn3283-3ubuntu2) ... (Reading database ... 11165 files and directories currently installed.) Preparing to replace python2.7-minimal 2.7.2-5ubuntu1 (using .../python2.7-minimal_2.7.2-5ubuntu1_armhf.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.2-5ubuntu1) ... (Reading database ... 11165 files and directories currently installed.) Preparing to replace xz-utils 5.1.1alpha+20110809-3 (using .../xz-utils_5.1.1alpha+20110809-3_armhf.deb) ... Unpacking replacement xz-utils ... Setting up xz-utils (5.1.1alpha+20110809-3) ... (Reading database ... 11159 files and directories currently installed.) Preparing to replace cpio 2.11-7ubuntu1 (using .../cpio_2.11-7ubuntu1_armhf.deb) ... Unpacking replacement cpio ... Preparing to replace initramfs-tools-bin 0.99ubuntu9 (using .../initramfs-tools-bin_0.99ubuntu9_armhf.deb) ... Unpacking replacement initramfs-tools-bin ... Preparing to replace procps 1:3.2.8-11ubuntu1 (using .../procps_1%3a3.2.8-11ubuntu4_armhf.deb) ... invoke-rc.d: policy-rc.d denied execution of stop. Unpacking replacement procps ... Preparing to replace udev 175-0ubuntu2 (using .../udev_175-0ubuntu2_armhf.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace advancecomp 1.15-1 (using .../advancecomp_1.15-1_armhf.deb) ... Unpacking replacement advancecomp ... Preparing to replace binutils 2.21.90.20111025-1ubuntu1 (using .../binutils_2.22-1ubuntu1_armhf.deb) ... Unpacking replacement binutils ... Preparing to replace cpp 4:4.6.1-2ubuntu5 (using .../cpp_4%3a4.6.1-2ubuntu5_armhf.deb) ... Unpacking replacement cpp ... Preparing to replace gcc 4:4.6.1-2ubuntu5 (using .../gcc_4%3a4.6.1-2ubuntu5_armhf.deb) ... Removing old gcc doc directory. Unpacking replacement gcc ... Preparing to replace g++ 4:4.6.1-2ubuntu5 (using .../g++_4%3a4.6.1-2ubuntu5_armhf.deb) ... Unpacking replacement g++ ... Preparing to replace make 3.81-8.1ubuntu1 (using .../make_3.81-8.1ubuntu1_armhf.deb) ... Unpacking replacement make ... Preparing to replace optipng 0.6.4-1 (using .../optipng_0.6.4-1_armhf.deb) ... Unpacking replacement optipng ... Preparing to replace pkgbinarymangler 106 (using .../pkgbinarymangler_109_all.deb) ... Unpacking replacement pkgbinarymangler ... Setting up libc-dev-bin (2.13-20ubuntu6) ... Setting up libc6-dev (2.13-20ubuntu6) ... Setting up libgdbm3 (1.8.3-10) ... Setting up perl (5.14.2-5ubuntu1) ... Setting up libffi6 (3.0.11~rc1-5) ... Setting up libpcre3 (8.12-4) ... Setting up libglib2.0-0 (2.30.1-2ubuntu1) ... Setting up module-init-tools (3.16-1ubuntu2) ... Setting up libmpc2 (0.9-4) ... Setting up cpio (2.11-7ubuntu1) ... Setting up initramfs-tools-bin (0.99ubuntu9) ... Setting up procps (1:3.2.8-11ubuntu4) ... Installing new version of config file /etc/init/procps.conf ... invoke-rc.d: policy-rc.d denied execution of start. Setting up udev (175-0ubuntu2) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up advancecomp (1.15-1) ... Setting up binutils (2.22-1ubuntu1) ... Setting up cpp (4:4.6.1-2ubuntu5) ... Setting up gcc (4:4.6.1-2ubuntu5) ... Setting up g++ (4:4.6.1-2ubuntu5) ... Setting up make (3.81-8.1ubuntu1) ... Setting up optipng (0.6.4-1) ... Setting up pkgbinarymangler (109) ... Installing new version of config file /etc/pkgbinarymangler/striptranslations.blacklist ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '9602b7344ff832c1eaf59509a0bed6aa938678f3', 'armhf', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '--purpose=PRIMARY', '--architecture=armhf', '--comp=universe', 'plink_1.07-1.dsc'] Initiating build 9602b7344ff832c1eaf59509a0bed6aa938678f3 with 2 processor cores. Automatic build of plink_1.07-1 on celbalrai by sbuild/armhf 1.170.5 Build started at 20111201-0839 ****************************************************************************** plink_1.07-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7), quilt, zlib1g-dev Checking for already installed source dependencies... debhelper: missing quilt: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper quilt zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libgettextpo0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl procmail graphviz Recommended packages: curl wget lynx-cur 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 libgettextpo0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 6405 kB of archives. After this operation, 19.3 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 libmagic1 file bsdmainutils gettext-base groff-base man-db html2text gettext intltool-debian po-debconf debhelper diffstat quilt zlib1g-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 armhf 1.2.0-5 [20.7 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main libxml2 armhf 2.7.8.dfsg-5ubuntu1 [550 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 armhf 0.6.2-2 [80.9 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 armhf 0.9.3-5 [393 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 armhf 5.09-2 [213 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main file armhf 5.09-2 [19.0 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils armhf 8.2.3 [193 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main groff-base armhf 1.21-6 [926 kB] Get:9 http://archive-team.internal/armhf/ precise/main libgettextpo0 armhf 0.18.1.1-5ubuntu2 [122 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main man-db armhf 2.6.0.2-3 [673 kB] Get:11 http://archive-team.internal/armhf/ precise/main gettext-base armhf 0.18.1.1-5ubuntu2 [133 kB] Get:12 http://archive-team.internal/armhf/ precise/main gettext armhf 0.18.1.1-5ubuntu2 [1818 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main html2text armhf 1.3.2a-15 [85.8 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main po-debconf armhf 1.0.16+nmu1ubuntu1 [211 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main debhelper armhf 8.9.9ubuntu1 [477 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main diffstat armhf 1.54-1 [20.2 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main quilt armhf 0.48-8 [279 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main zlib1g-dev armhf 1:1.2.3.4.dfsg-3ubuntu4 [158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6405 kB in 2s (2294 kB/s) Selecting previously unselected package libpipeline1. (Reading database ... 11010 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armhf.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5ubuntu1_armhf.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armhf.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu2_armhf.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5ubuntu2_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-3_armhf.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5ubuntu2_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1ubuntu1_armhf.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.9ubuntu1_armhf.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.54-1_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../quilt_0.48-8_armhf.deb) ... Selecting previously unselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu4_armhf.deb) ... Setting up libpipeline1 (1.2.0-5) ... Setting up libxml2 (2.7.8.dfsg-5ubuntu1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu2) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... 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 gettext-base (0.18.1.1-5ubuntu2) ... Setting up groff-base (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1ubuntu1) ... Setting up debhelper (8.9.9ubuntu1) ... Setting up diffstat (1.54-1) ... Setting up quilt (0.48-8) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.13-20ubuntu6 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu1 gcc-4.6_4.6.2-5ubuntu1 g++-4.6_4.6.2-5ubuntu1 binutils_2.22-1ubuntu1 libstdc++6-4.6-dev_4.6.2-5ubuntu1 libstdc++6_4.6.2-5ubuntu1 ------------------------------------------------------------------------------ gpgv: Signature made Fri Oct 23 12:33:43 2009 UTC 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 dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2 dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro dpkg-buildpackage: source package plink dpkg-buildpackage: source version 1.07-1 dpkg-source --before-build plink-1.07 dpkg-buildpackage: host architecture armhf /usr/bin/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/buildd/plink-1.07' rm -f *.o *~ make[1]: Leaving directory `/build/buildd/plink-1.07' dh_clean build-stamp install-stamp plink debian/rules build QUILT_PATCHES=debian/patches \ quilt --quiltrc /dev/null push -a || test $? = 2 /usr/bin/make CXXFLAGS='-Wall -g -O2 -DWITH_R_PLUGINS -DUNIX' FORCE_DYNAMIC=1 make[1]: Entering directory `/build/buildd/plink-1.07' g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c plink.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 options.cpp In file included from options.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from plink.cpp:28:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from plink.cpp:35:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from plink.cpp:40:0: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp: In function 'int main(int, char**)': plink.cpp:764:13: warning: suggest parentheses around '&&' within '||' [-Wparentheses] plink.cpp:2106:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp: In member function 'void Plink::cleanUp()': plink.cpp:2359:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp:2362:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp:2366:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c input.cpp In file included from input.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readData()': input.cpp:516:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:521:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:545:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:579:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:595:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:611:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:631:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readSet()': input.cpp:695:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readClusterFile(bool)': input.cpp:787:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:817:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:821:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readPhenoFile()': input.cpp:897:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:927:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:961:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:965:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1037:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1043:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1064:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::makePhenotype()': input.cpp:1208:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readCovariateFile()': input.cpp:1232:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1256:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1261:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readCovListFile()': input.cpp:1335:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1374:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1519:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1538:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readMultiplePhenoFile()': input.cpp:1572:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1599:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1602:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1745:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1764:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readSegmentFile(std::ifstream&)': input.cpp:1792:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': input.cpp:2116:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2172:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2200:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2210:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2215:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2225:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readFamFile(std::string)': input.cpp:2389:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2397:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2419:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2453:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': input.cpp:2471:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::updateAlleles()': input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c binput.cpp In file included from binput.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:157:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:176:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:186:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:261:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:339:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:351:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:398:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readData()': input.cpp:343:44: warning: 'PED' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tinput.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genome.cpp In file included from tinput.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:218:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:246:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:256:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:261:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:271:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:309:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:591:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:603:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genome.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c helper.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c stats.cpp In file included from helper.h:24:0, from helper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::string displayLine(std::vector >&)': helper.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void display(matrix_t&)': helper.cpp:76:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:79:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void display(vector_t&)': helper.cpp:90:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void display(std::vector&)': helper.cpp:100:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': helper.cpp:193:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'std::vector > CArgs::value(std::string, int)': helper.cpp:277:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector > parse2str(std::string)': helper.cpp:306:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:307:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:309:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector parse2int(std::string)': helper.cpp:323:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': helper.cpp:461:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from helper.h:24:0, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void summaryBasics(Plink&)': helper.cpp:595:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:611:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'double genotypingRate(Plink&, int)': helper.cpp:659:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:664:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:729:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void removeMissingPhenotypes(Plink&)': helper.cpp:775:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void geno2matrix(std::vector&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::string chromosomeName(int)': helper.cpp:952:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'int getMarkerChromosome(Plink&, std::string)': helper.cpp:959:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'int getMarkerNumber(Plink&, std::string)': helper.cpp:966:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'bool seeChromosome(Plink&, int)': helper.cpp:973:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector getChromosomeRange(Plink&)': helper.cpp:1040:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void checkFileExists(std::vector >)': helper.cpp:1172:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::prettyPrintLengths()': helper.cpp:1264:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:1267:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:1273:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:1391:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp:1483:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp:1515:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp:1521:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2462:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2491:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnCase()': helper.cpp:2510:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnControl()': helper.cpp:2530:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnMale()': helper.cpp:2549:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnFemale()': helper.cpp:2568:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnFounder()': helper.cpp:2587:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnNonFounder()': helper.cpp:2606:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::attribFilterSNP()': helper.cpp:2638:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2671:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::attribFilterInd()': helper.cpp:2722:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2756:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void makePersonMap(Plink&, std::map, Individual*>&)': helper.cpp:2935:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void smoother(Plink&, vector_t&, int, vector_t&, vector_t&, std::vector&)': helper.cpp:2959:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::map, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] helper.cpp: In function 'double getDouble(std::string, std::string)': helper.cpp:407:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': helper.cpp:393:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In function 'int getInt(std::string, std::string)': helper.cpp:380:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'double CArgs::value_double(std::string)': helper.cpp:256:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': helper.cpp:244:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'int CArgs::value_int(std::string)': helper.cpp:232:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'std::string CArgs::value(std::string)': helper.cpp:219:1: warning: control reaches end of non-void function [-Wreturn-type] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c filters.cpp In file included from filters.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:123:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:132:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:155:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:163:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:198:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:273:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] filters.cpp:591:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:611:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:739:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:762:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1078:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1091:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1143:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1165:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] filters.cpp: In member function 'void Plink::thinSNPs()': filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c locus.cpp In file included from locus.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c multi.cpp In file included from multi.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c crandom.cpp multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:304:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:357:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:372:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:154:8: warning: unused variable 'is0zero' [-Wunused-variable] multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cluster.cpp In file included from helper.h:24:0, from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:452:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:511:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:492:8: warning: unused variable 'size' [-Wunused-variable] cluster.cpp:626:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:648:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:651:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:784:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:786:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:919:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:954:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:955:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:975:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:976:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1038:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1041:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1049:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1050:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1060:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1061:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1107:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1110:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1133:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1163:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1169:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'double cldist(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1204:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'double groupAvgLink(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1228:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1229:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'bool homogeneous_clusters(Plink&, std::vector&, std::vector&)': cluster.cpp:1254:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1255:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'bool spec_clusters(Plink&, std::vector&, std::vector&)': cluster.cpp:1272:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1276:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'bool pairable_cluster(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1290:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1291:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In member function 'void Plink::groupGenome()': cluster.cpp:1643:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1661:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1664:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mds.cpp In file included from mds.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp:191:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp:279:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c output.cpp In file included from output.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:86:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:89:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::display_twolocus()': output.cpp:402:28: warning: variable 'loc1' set but not used [-Wunused-but-set-variable] output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:526:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:553:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::keep2SetsForGenome()': output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] output.cpp: In member function 'void Plink::outputSetFile()': output.cpp:2200:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:2322:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::setTable()': output.cpp:2367:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:2380:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::writeSetFile()': output.cpp:2409:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:2412:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::display_pairList()': output.cpp:145:65: warning: 'i2' may be used uninitialized in this function [-Wuninitialized] output.cpp:144:65: warning: 'i1' may be used uninitialized in this function [-Wuninitialized] output.cpp: In member function 'void Plink::display_indivReport()': output.cpp:69:36: warning: 'i1' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c informative.cpp In file included from informative.cpp:18:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] informative.cpp:102:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] informative.cpp:105:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c assoc.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c epi.cpp In file included from helper.h:24:0, from assoc.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from assoc.cpp:29:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': assoc.cpp:395:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:741:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:744:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:785:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:788:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] In file included from epi.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp:154:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp:161:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp:438:12: warning: unused variable 'zero' [-Wunused-variable] epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c prephap.cpp In file included from prephap.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from prephap.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp: In member function 'void HaploPhase::readTagFile()': prephap.cpp:226:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:283:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:412:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:416:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:420:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:470:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp: In member function 'void HaploPhase::makeSlidingWindow(std::string)': prephap.cpp:533:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:560:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c phase.cpp In file included from phase.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from phase.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from phase.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': phase.cpp:373:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'void HaploPhase::enumerateHaplotypes(std::vector&)': phase.cpp:472:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'void HaploPhase::performAlternEM()': phase.cpp:678:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1187:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1238:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1280:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1299:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1575:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1843:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c trio.cpp In file included from trio.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:272:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:335:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:342:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:350:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:474:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:492:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:504:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:871:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:882:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:895:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:931:6: warning: unused variable 'tmp' [-Wunused-variable] trio.cpp:936:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:943:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:1048:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In member function 'void Plink::makeMissingParents()': trio.cpp:1236:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:1245:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tdt.cpp In file included from tdt.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] tdt.cpp:132:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:144:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:210:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:234:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:327:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:330:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:412:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:415:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:557:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:668:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:776:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sharing.cpp tdt.cpp:937:58: warning: 'zt' may be used uninitialized in this function [-Wuninitialized] In file included from perm.h:17:0, from sharing.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genepi.cpp In file included from genepi.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp: In function 'double C(int, double, double)': genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] genepi.cpp: In function 'long double pillai(int, int, int, double)': genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:489:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:497:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:506:10: warning: unused variable 'n12' [-Wunused-variable] genepi.cpp:507:10: warning: unused variable 'ne' [-Wunused-variable] genepi.cpp: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': genepi.cpp:1025:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:1033:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:1043:10: warning: unused variable 'n12' [-Wunused-variable] genepi.cpp:1044:10: warning: unused variable 'ne' [-Wunused-variable] genepi.cpp:1064:10: warning: unused variable 'nind' [-Wunused-variable] genepi.cpp: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sets.cpp In file included from sets.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:840:83: warning: 'cancor1_pos' may be used uninitialized in this function [-Wuninitialized] In file included from sets.cpp:24:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::sizeSets()': sets.cpp:37:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:52:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:59:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:62:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::pruneMC(Plink&, bool, double)': sets.cpp:129:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:176:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::dropNotSet(Plink&)': sets.cpp:216:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:218:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:236:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:237:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::makeLDSets()': sets.cpp:317:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:323:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:329:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:332:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:367:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:370:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:413:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:619:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:631:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:632:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:642:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:643:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::profileTestScore()': sets.cpp:703:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:713:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)': sets.cpp:905:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:975:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::fitStepwiseModel()': sets.cpp:1042:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c perm.cpp In file included from perm.h:17:0, from perm.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp:145:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp: In member function 'void Perm::setOriginalRanking(vector_t&)': perm.cpp:187:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp:199:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp: In member function 'bool Perm::update(std::vector&, std::vector&)': perm.cpp:273:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mh.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genedrop.cpp In file included from perm.h:17:0, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mh.cpp:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] In file included from perm.h:17:0, from genedrop.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genedrop.cpp: In member function 'void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c gxe.cpp In file included from helper.h:24:0, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c merge.cpp In file included from merge.cpp:22:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:377:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:395:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:403:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:426:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:722:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:733:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:784:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:830:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:842:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c hotel.cpp merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wuninitialized] In file included from hotel.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] hotel.cpp:173:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c multiple.cpp In file included from helper.h:24:0, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multiple.cpp:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c haploCC.cpp In file included from haploCC.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haploCC.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp: In member function 'void HaploPhase::haplotypicCC(std::map&, int, bool)': haploCC.cpp:48:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:62:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] haploCC.cpp:79:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:93:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:357:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] haploCC.cpp:375:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:392:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c haploTDT.cpp In file included from haploTDT.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haploTDT.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c poo.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c webcheck.cpp In file included from poo.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:195:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:198:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': poo.cpp:293:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:328:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:239:10: warning: unused variable 'zt' [-Wunused-variable] In file included from helper.h:24:0, from webcheck.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:130:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:146:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:180:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:218:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c qfam.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c linear.cpp In file included from helper.h:24:0, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:89:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:97:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:315:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': qfam.cpp:505:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:648:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:657:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] In file included from helper.h:24:0, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linear.cpp: In member function 'double LinearModel::getPValue()': linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:100:18: warning: 'irow' may be used uninitialized in this function [-Wuninitialized] linear.cpp:101:18: warning: 'icol' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c bmerge.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c parse.cpp In file included from bmerge.cpp:22:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] bmerge.cpp:357:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:390:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:409:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:417:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:440:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from parse.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:549:11: warning: variable 'indn' set but not used [-Wunused-but-set-variable] bmerge.cpp:697:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] bmerge.cpp:839:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:871:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:883:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c mishap.cpp In file included from mishap.cpp:17:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from mishap.cpp:20:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp: In member function 'void Plink::performMisHapTests()': mishap.cpp:209:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp:236:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp:349:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp:373:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c legacy.cpp In file included from helper.h:24:0, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:377:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:381:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:384:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:390:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:395:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:415:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:424:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:460:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:461:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:462:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:467:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:480:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': legacy.cpp:203:27: warning: 'last' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c homozyg.cpp In file included from helper.h:24:0, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:695:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:722:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:756:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:773:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:861:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1178:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1331:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1437:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1441:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1461:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:24: warning: value computed is not used [-Wunused-value] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c segment.cpp In file included from helper.h:24:0, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:15: warning: unused variable 'p1' [-Wunused-variable] segment.cpp:955:15: warning: unused variable 'p2' [-Wunused-variable] segment.cpp:1027:19: warning: unused variable 'p1' [-Wunused-variable] segment.cpp:1028:19: warning: unused variable 'p2' [-Wunused-variable] segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] segment.cpp: In member function 'void Plink::indivSegmentSummary()': segment.cpp:1855:14: warning: variable 'p' set but not used [-Wunused-but-set-variable] segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2380:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2382:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2412:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2414:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2416:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2443:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2445:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2447:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2474:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2476:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2478:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c model.cpp In file included from model.cpp:15:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from model.cpp:17:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp: In member function 'void Model::setMissing(std::vector&)': model.cpp:132:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp:367:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp:374:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:850:1: warning: control reaches end of non-void function [-Wreturn-type] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c logistic.cpp In file included from helper.h:24:0, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] logistic.cpp: In member function 'double LogisticModel::getPValue()': logistic.cpp:327:8: warning: unused variable 'okay' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c glm.cpp In file included from helper.h:24:0, from glm.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from glm.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp: In member function 'vector_t Plink::glmAssoc(bool, Perm&)': glm.cpp:294:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:344:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:355:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:423:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:610:37: warning: 'df' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c dcdflib.cpp dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:1882:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:55: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:60: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dcdflib.cpp:6088:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp:6112:52: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp:6153:52: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dcdflib.cpp: In function 'double dt1(double*, double*, double*)': dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:64: warning: suggest parentheses around '&&' within '||' [-Wparentheses] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c elf.cpp In file included from helper.h:24:0, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp:939:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:400:48: warning: 'wt' may be used uninitialized in this function [-Wuninitialized] elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1142:19: warning: 'p_gcnt' may be used uninitialized in this function [-Wuninitialized] elf.cpp:1165:15: warning: 'p_cnt' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c dfam.cpp In file included from dfam.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:86:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:96:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:106:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:157:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:240:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dfam.cpp:271:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:378:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:218:9: warning: unused variable 'informative' [-Wunused-variable] dfam.cpp:504:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c fisher.cpp In file included from helper.h:24:0, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:61: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:267:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:273:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:450:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:501:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:509:54: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:563:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:751:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1539:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:1555:52: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:1597:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c linput.cpp In file included from linput.cpp:25:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:136:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:146:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:164:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:200:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:209:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c sockets.cpp In file included from helper.h:24:0, from sockets.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c lookup.cpp In file included from helper.h:24:0, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup.cpp:203:8: warning: unused variable 'totalSNPs' [-Wunused-variable] lookup.cpp:204:8: warning: unused variable 'gcount' [-Wunused-variable] lookup.cpp:272:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup.cpp:289:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c proxy.cpp In file included from proxy.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from proxy.cpp:24:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:314:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:332:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:854:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:1332:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:1401:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] proxy.cpp:939:58: warning: 'ref' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c pdriver.cpp In file included from pdriver.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from pdriver.cpp:18:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] pdriver.cpp: In member function 'void Plink::proxyWrapper()': pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c haploQTL.cpp In file included from haploQTL.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haploQTL.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploQTL.cpp: In member function 'void HaploPhase::haplotypicQTL(std::map&, int, bool)': haploQTL.cpp:83:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploQTL.cpp:145:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c haplohelper.cpp In file included from haplohelper.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplohelper.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplohelper.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::imputeAllHaplotypes()': haplohelper.cpp:104:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:134:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::setTestHaplotype(std::string)': haplohelper.cpp:337:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::reportPhase()': haplohelper.cpp:396:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:413:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::reportPhaseWideFormat()': haplohelper.cpp:487:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'double HaploPhase::imputeHaplotypes(int, bool&, bool&)': haplohelper.cpp:754:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:802:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'double HaploPhase::rsq_internal(boolvec_t&, boolvec_t&, boolvec_t&, boolvec_t&)': haplohelper.cpp:850:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:850:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:850:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:851:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:957:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1251:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1252:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1477:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c haplowindow.cpp In file included from haplowindow.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplowindow.cpp:27:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplowindow.cpp:28:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': haplowindow.cpp:48:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::prunePhase(int, double)': haplowindow.cpp:558:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:574:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:691:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:751:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:791:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:798:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:868:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:872:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::reportPhase()': haplowindow.cpp:949:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:966:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genogroup.cpp In file included from genogroup.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genogroup.cpp:24:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genogroup.cpp:28:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c nonfounderphasing.cpp In file included from nonfounderphasing.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from nonfounderphasing.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from nonfounderphasing.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nonfounderphasing.cpp: In member function 'void HaploPhase::phaseAndScoreNonfounder(int)': nonfounderphasing.cpp:668:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c clumpld.cpp In file included from helper.h:24:0, from clumpld.h:21, from clumpld.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from clumpld.cpp:21:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp: In member function 'std::vector clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:137:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:173:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:201:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:204:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:480:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:520:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:611:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:1097:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c genoerr.cpp In file included from genoerr.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genoerr.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genoerr.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp: In member function 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)': genoerr.cpp:157:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:189:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:190:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:225:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:315:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:328:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:347:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:358:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c em.cpp In file included from em.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from em.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from em.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp: In member function 'void HaploPhase::performEM_original()': em.cpp:89:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:97:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:106:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:128:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:132:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:162:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:166:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c impute.cpp In file included from impute.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from impute.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from impute.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp: In constructor 'probabilisticGenotype::probabilisticGenotype()': impute.cpp:40:25: warning: suggest parentheses around assignment used as truth value [-Wparentheses] impute.cpp: In member function 'void HaploPhase::updateForImputation()': impute.cpp:105:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp:144:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp:161:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp:313:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c metaem.cpp In file included from metaem.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from metaem.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from metaem.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaem.cpp: In member function 'void HaploPhase::enumeratePhasedWindows(int)': metaem.cpp:239:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c profile.cpp In file included from profile.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] profile.cpp:390:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp:402:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp:421:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] profile.cpp:629:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp: In function 'void scoreRanges(int, std::vector&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c nlist.cpp In file included from helper.h:24:0, from nlist.h:21, from nlist.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector NList::expandNumberList(std::vector&)': nlist.cpp:107:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:124:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:151:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:160:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector > NList::tokenize(std::string)': nlist.cpp:189:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:239:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:253:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c whap.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c simul.cpp In file included from helper.h:24:0, from whap.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from whap.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In member function 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)': whap.cpp:334:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:393:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:454:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:456:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:508:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:511:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:619:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:670:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:793:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:793:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:986:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1015:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1048:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1118:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1129:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1142:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1162:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1197:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1231:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1290:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1326:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1334:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In member function 'void Chap::setSNPList(std::vector&, ChapModel&)': whap.cpp:1389:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In function 'void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)': whap.cpp:1425:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1434:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from helper.h:24:0, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp:679:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp: In member function 'void Plink::simulateSNPs_QT()': simul.cpp:1146:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp:1211:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp:1358:23: warning: unused variable 'cumU' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c gvar.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cnv.cpp In file included from helper.h:24:0, from gvar.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:192:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:247:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:298:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:381:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:395:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:403:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:471:11: warning: unused variable 'ip' [-Wunused-variable] gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] gvar.cpp:549:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:553:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:556:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from helper.h:24:0, from cnv.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:8: warning: unused variable 'p1' [-Wunused-variable] cnv.cpp:247:11: warning: unused variable 'p2' [-Wunused-variable] cnv.cpp:332:12: warning: unused variable 'p1' [-Wunused-variable] cnv.cpp:332:15: warning: unused variable 'p2' [-Wunused-variable] cnv.cpp:678:36: warning: variable 'is' set but not used [-Wunused-but-set-variable] cnv.cpp:815:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp:825:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp:1031:25: warning: variable 'i2' set but not used [-Wunused-but-set-variable] cnv.cpp:1103:36: warning: variable 'il' set but not used [-Wunused-but-set-variable] cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:20: warning: statement has no effect [-Wunused-value] cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c step.cpp In file included from helper.h:24:0, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c greport.cpp In file included from greport.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:147:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:156:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:169:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:240:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c flip.cpp In file included from helper.h:24:0, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c qualscores.cpp In file included from helper.h:24:0, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cnvqt.cpp In file included from helper.h:24:0, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c cfamily.cpp In file included from cfamily.cpp:18:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:221:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:237:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:276:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:288:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c setscreen.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c idhelp.cpp In file included from setscreen.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp:110:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp:188:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp:196:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from idhelp.cpp:18:0: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from idhelp.cpp:19:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:63:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'bool IDHelper::matchIndividual(IDGroup*, std::map >&)': idhelp.cpp:136:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:169:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:221:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:296:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] idhelp.cpp: In member function 'std::set IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:510:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:542:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:547:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:553:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:529:10: warning: unused variable 'seenJoint' [-Wunused-variable] idhelp.cpp:584:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:594:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:678:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:727:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:742:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:745:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:747:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:757:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] idhelp.cpp:772:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:790:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:794:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:808:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:836:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:888:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:894:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:903:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:922:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:950:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:975:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1000:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1003:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1013:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] idhelp.cpp:1025:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1028:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1031:14: warning: unused variable 'v' [-Wunused-variable] idhelp.cpp:1070:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1085:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1110:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1128:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1183:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1189:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1236:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1242:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1245:14: warning: unused variable 'v' [-Wunused-variable] idhelp.cpp:1346:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1424:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1440:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1631:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1648:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1649:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1654:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1675:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1684:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1692:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1710:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1733:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1735:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1770:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1784:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1801:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1903:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1937:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1957:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1964:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1986:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2018:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2024:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2030:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2034:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2070:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] idhelp.cpp:2167:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2168:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2201:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2234:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c tag.cpp In file included from helper.h:24:0, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c hapglm.cpp In file included from helper.h:24:0, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from hapglm.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c lookup2.cpp In file included from helper.h:24:0, from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp:203:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp:280:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp:325:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c blox.cpp In file included from blox.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from blox.cpp:23:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] blox.cpp: In member function 'std::map > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] blox.cpp:418:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] blox.cpp:427:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] blox.cpp:123:16: warning: unused variable 'fourGameteCutoff' [-Wunused-variable] blox.cpp: In member function 'void PairwiseLinkage::calculateCI()': blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] blox.cpp:570:3: warning: 'pB2' may be used uninitialized in this function [-Wuninitialized] blox.cpp:505:21: warning: 'pB1' may be used uninitialized in this function [-Wuninitialized] blox.cpp:503:21: warning: 'pA2' may be used uninitialized in this function [-Wuninitialized] blox.cpp:503:21: warning: 'pA1' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c zed.cpp In file included from helper.h:24:0, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c dosage.cpp In file included from dosage.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from dosage.cpp:23:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c annot.cpp dosage.cpp: In member function 'void Plink::processDosageFile()': dosage.cpp:110:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:513:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:548:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:581:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:601:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:695:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:750:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:989:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:1170:11: warning: unused variable 'statistic' [-Wunused-variable] dosage.cpp:1252:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:1310:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] In file included from annot.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:250:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:251:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:260:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:275:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:300:9: warning: unused variable 'include' [-Wunused-variable] dosage.cpp:1179:31: warning: 'snp_code' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c metaanal.cpp In file included from metaanal.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp: In constructor 'Alleles::Alleles(std::string, int, int, std::string, std::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] metaanal.cpp:44:10: warning: 'std::string Alleles::a1' [-Wreorder] metaanal.cpp:61:3: warning: when initialized here [-Wreorder] metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:182:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:203:23: warning: statement has no effect [-Wunused-value] metaanal.cpp:213:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:235:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:261:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:300:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] metaanal.cpp:482:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:637:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:680:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c r.cpp In file included from Rconnection.h:42:0, from r.cpp:29: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] In file included from helper.h:24:0, from r.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from r.cpp:29:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h:249:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wuninitialized] r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c Rconnection.cpp In file included from Rconnection.h:42:0, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] In file included from Rconnection.cpp:30:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h:249:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -c zfstream.cpp g++ -Wall -g -O2 -DWITH_R_PLUGINS -DUNIX -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[1]: Leaving directory `/build/buildd/plink-1.07' touch build-stamp /usr/bin/fakeroot debian/rules binary-arch # nothing to do, the single binary is taken directly touch install-stamp dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* dh_install dh_installman dh_link dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: plink dh_strip debug symbol extraction: packages to act on: plink dh_strip debug symbol extraction: ignored packages: dpkg-deb: building package `plink-dbgsym' in `../plink-dbgsym_1.07-1_armhf.ddeb'. dh_compress dh_fixperms dh_installdeb dh_shlibdeps dpkg-shlibdeps: warning: debian/plink/usr/lib/plink/plink contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 109 pkgstriptranslations: processing plink (in debian/plink); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/plink/DEBIAN/control, package plink, directory debian/plink dpkg-deb: warning: 'debian/plink/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `plink' in `../plink_1.07-1_armhf.deb'. dpkg-genchanges -B -mUbuntu/armel Build Daemon >../plink_1.07-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build plink-1.07 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20111201-0902 Publishing debug debs. chroot-autobuild/build/buildd/plink_1.07-1_armhf.deb: new debian package, version 2.0. size 1119730 bytes: control archive= 1103 bytes. 1120 bytes, 26 lines control 534 bytes, 8 lines md5sums Package: plink Version: 1.07-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1819 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Description: whole-genome association analysis toolset plink expects as input the data from SNP (single nucleotide polymorphism) chips of many individuals and their phenotypical description of a disease. It finds associations of single or pairs of DNA variations with a phenotype and can retrieve SNP annotation from an online source. . SNPs can evaluated individually or as pairs for their association with the disease phenotypes. The joint investigation of copy number variations is supported. A variety of statistical tests have been implemented. . Please note: The executable was renamed to p-link because of a name clash. Please read more about this in /usr/share/doc/README.Debian. chroot-autobuild/build/buildd/plink_1.07-1_armhf.deb: drwxr-xr-x root/root 0 2011-12-01 09:02 ./ drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/ drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/lib/ drwxr-xr-x root/root 0 2011-12-01 09:02 ./usr/lib/plink/ -rwxr-xr-x root/root 1806628 2011-12-01 09:02 ./usr/lib/plink/plink drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/bin/ drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/share/ drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/share/man/ drwxr-xr-x root/root 0 2011-12-01 09:02 ./usr/share/man/man1/ -rw-r--r-- root/root 672 2011-12-01 09:01 ./usr/share/man/man1/p-link.1.gz drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-12-01 09:02 ./usr/share/doc/plink/ -rw-r--r-- root/root 980 2011-12-01 08:40 ./usr/share/doc/plink/changelog.Debian.gz -rw-r--r-- root/root 1563 2011-12-01 08:40 ./usr/share/doc/plink/copyright drwxr-xr-x root/root 0 2011-12-01 09:01 ./usr/share/doc/plink/examples/ -rw-r--r-- root/root 23 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.map -rw-r--r-- root/root 138 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.ped -rw-r--r-- root/root 1590 2011-12-01 08:40 ./usr/share/doc/plink/README.Debian -rw-r--r-- root/root 1287 2007-07-27 14:51 ./usr/share/doc/plink/README.txt lrwxrwxrwx root/root 0 2011-12-01 09:01 ./usr/bin/p-link -> ../lib/plink/plink plink_1.07-1_armhf.changes: Format: 1.8 Date: Fri, 23 Oct 2009 13:35:02 +0200 Source: plink Binary: plink Architecture: armhf Version: 1.07-1 Distribution: precise Urgency: low Maintainer: Ubuntu/armel Build Daemon Changed-By: Andreas Tille Description: plink - whole-genome association analysis toolset Changes: plink (1.07-1) unstable; urgency=low . * New upstream version * Removed debian/patches/20_plink-1.06-gcc4.4.patch because it is applied upstream * Standards-Version: 3.8.3 (no changes needed) * Debhelper 7 * Build-Depends: zlib1g-dev Checksums-Sha1: d8c9a82ca8fb7adcb41255e571298394f6f80732 1119730 plink_1.07-1_armhf.deb Checksums-Sha256: c5b9dc41182d7bf6dd48e1e5c068d54fbe015bcba5eea346c7ed546cd7b67ccb 1119730 plink_1.07-1_armhf.deb Files: 0c97cf5d7b52fdfa43d1b8b5ab732771 1119730 science optional plink_1.07-1_armhf.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/plink-1.07 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge intltool-debian groff-base gettext file zlib1g-dev diffstat html2text gettext-base debhelper po-debconf libunistring0 quilt libcroco3 libmagic1 libpipeline1 libxml2 bsdmainutils libgettextpo0 man-db (Reading database ... 12344 files and directories currently installed.) Removing zlib1g-dev ... Removing debhelper ... Removing po-debconf ... Removing quilt ... Purging configuration files for quilt ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing intltool-debian ... Removing groff-base ... Purging configuration files for groff-base ... Removing gettext ... Removing file ... Removing diffstat ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing libgettextpo0 ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20111201-0902 Build needed 00:22:13, 133120k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '9602b7344ff832c1eaf59509a0bed6aa938678f3'] Scanning for processes to kill in build /home/buildd/build-9602b7344ff832c1eaf59509a0bed6aa938678f3/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '9602b7344ff832c1eaf59509a0bed6aa938678f3'] Unmounting chroot for build 9602b7344ff832c1eaf59509a0bed6aa938678f3... none /home/buildd/build-9602b7344ff832c1eaf59509a0bed6aa938678f3/chroot-autobuild/proc proc rw,relatime 0 0 none /home/buildd/build-9602b7344ff832c1eaf59509a0bed6aa938678f3/chroot-autobuild/dev/pts devpts rw,relatime,mode=600 0 0 none /home/buildd/build-9602b7344ff832c1eaf59509a0bed6aa938678f3/chroot-autobuild/sys sysfs rw,relatime 0 0 none /home/buildd/build-9602b7344ff832c1eaf59509a0bed6aa938678f3/chroot-autobuild/dev/shm tmpfs rw,relatime 0 0 RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '9602b7344ff832c1eaf59509a0bed6aa938678f3'] Removing build 9602b7344ff832c1eaf59509a0bed6aa938678f3