RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux denneed01 3.13.0-8-generic #28-Ubuntu SMP Tue Feb 11 17:58:07 UTC 2014 ppc64le Buildd toolchain package versions: launchpad-buildd_121~0.IS.08.04.0 python-lpbuildd_121~0.IS.08.04.0 dpkg-dev_1.17.5ubuntu4. Syncing the system clock with the buildd NTP service... 19 Feb 12:51:58 ntpdate[25440]: adjust time server 10.211.37.1 offset 0.000222 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5604159', '/home/buildd/filecache-default/1418c9e5f0eb143d9f77e4665c5b7c89c42011cc'] Unpacking chroot for build PACKAGEBUILD-5604159 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5604159'] Mounting chroot for build PACKAGEBUILD-5604159 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5604159', 'deb http://ftpmaster.internal/ubuntu trusty main universe'] Overriding sources.list in build-PACKAGEBUILD-5604159 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5604159', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-5604159 Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty Release.gpg Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Hit http://archive-team.internal trusty Release Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Ign http://archive-team.internal trusty/main ppc64el Packages/DiffIndex Get:3 http://ftpmaster.internal trusty Release [58.5 kB] Get:4 http://ftpmaster.internal trusty Release [58.5 kB] Get:5 http://ftpmaster.internal trusty/main ppc64el Packages [1222 kB] Ign http://archive-team.internal trusty/main Translation-en Hit http://archive-team.internal trusty/main ppc64el Packages Get:6 http://ftpmaster.internal trusty/universe ppc64el Packages [4398 kB] Get:7 http://ftpmaster.internal trusty/main Translation-en [761 kB] Get:8 http://ftpmaster.internal trusty/universe Translation-en [4058 kB] Get:9 http://ftpmaster.internal trusty/main ppc64el Packages [1226 kB] Get:10 http://ftpmaster.internal trusty/universe ppc64el Packages [5005 kB] Get:11 http://ftpmaster.internal trusty/main Translation-en [760 kB] Get:12 http://ftpmaster.internal trusty/universe Translation-en [4056 kB] Fetched 21.6 MB in 21s (1019 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: cpp-4.8 dash e2fslibs e2fsprogs g++-4.8 gcc-4.8 gcc-4.8-base gcc-4.9-base libasn1-8-heimdal libatomic1 libcomerr2 libgcc-4.8-dev libgcc1 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal libroken18-heimdal libss2 libstdc++-4.8-dev libstdc++6 libwind0-heimdal linux-libc-dev 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After this operation, 137 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main dash ppc64el 0.5.7-4ubuntu1 [94.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main e2fslibs ppc64el 1.42.9-3ubuntu1 [185 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main e2fsprogs ppc64el 1.42.9-3ubuntu1 [662 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libitm1 ppc64el 4.8.2-16ubuntu1 [28.8 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libgomp1 ppc64el 4.8.2-16ubuntu1 [21.9 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main g++-4.8 ppc64el 4.8.2-16ubuntu1 [6242 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8 ppc64el 4.8.2-16ubuntu1 [4809 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main cpp-4.8 ppc64el 4.8.2-16ubuntu1 [4425 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libatomic1 ppc64el 4.8.2-16ubuntu1 [7868 B] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.9-base ppc64el 4.9-20140217-0ubuntu1 [14.3 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libgcc1 ppc64el 1:4.9-20140217-0ubuntu1 [29.1 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++-4.8-dev ppc64el 4.8.2-16ubuntu1 [1087 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libgcc-4.8-dev ppc64el 4.8.2-16ubuntu1 [245 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8-base ppc64el 4.8.2-16ubuntu1 [14.8 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++6 ppc64el 4.8.2-16ubuntu1 [270 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libcomerr2 ppc64el 1.42.9-3ubuntu1 [62.4 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libss2 ppc64el 1.42.9-3ubuntu1 [66.5 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libroken18-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libasn1-8-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [132 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libhcrypto4-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [90.1 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main libheimbase1-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [28.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libwind0-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [47.8 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libhx509-5-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [97.8 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libkrb5-26-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [188 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libheimntlm0-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [15.7 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main libgssapi3-heimdal ppc64el 1.6~git20131207+dfsg-1ubuntu1 [83.6 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main linux-libc-dev ppc64el 3.13.0-10.30 [754 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.7 MB in 17s (1140 kB/s) (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../dash_0.5.7-4ubuntu1_ppc64el.deb ... Unpacking dash (0.5.7-4ubuntu1) over (0.5.7-3ubuntu1) ... Setting up dash (0.5.7-4ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking e2fslibs:ppc64el (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up e2fslibs:ppc64el (1.42.9-3ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking e2fsprogs (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up e2fsprogs (1.42.9-3ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libitm1_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libitm1:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../libgomp1_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libgomp1:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../g++-4.8_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking g++-4.8 (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../gcc-4.8_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking gcc-4.8 (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../cpp-4.8_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking cpp-4.8 (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../libatomic1_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libatomic1:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../gcc-4.9-base_4.9-20140217-0ubuntu1_ppc64el.deb ... Unpacking gcc-4.9-base:ppc64el (4.9-20140217-0ubuntu1) over (4.9-20140213-0ubuntu2) ... Setting up gcc-4.9-base:ppc64el (4.9-20140217-0ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a4.9-20140217-0ubuntu1_ppc64el.deb ... Unpacking libgcc1:ppc64el (1:4.9-20140217-0ubuntu1) over (1:4.9-20140213-0ubuntu2) ... Setting up libgcc1:ppc64el (1:4.9-20140217-0ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libstdc++-4.8-dev_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libstdc++-4.8-dev:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../libgcc-4.8-dev_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libgcc-4.8-dev:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Preparing to unpack .../gcc-4.8-base_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking gcc-4.8-base:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Setting up gcc-4.8-base:ppc64el (4.8.2-16ubuntu1) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.8.2-16ubuntu1_ppc64el.deb ... Unpacking libstdc++6:ppc64el (4.8.2-16ubuntu1) over (4.8.2-15ubuntu3) ... Setting up libstdc++6:ppc64el (4.8.2-16ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking libcomerr2:ppc64el (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up libcomerr2:ppc64el (1.42.9-3ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libss2_1.42.9-3ubuntu1_ppc64el.deb ... Unpacking libss2:ppc64el (1.42.9-3ubuntu1) over (1.42.9-2ubuntu1) ... Setting up libss2:ppc64el (1.42.9-3ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libroken18-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libroken18-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libasn1-8-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libasn1-8-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libhcrypto4-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libhcrypto4-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libheimbase1-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libheimbase1-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libwind0-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libwind0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libhx509-5-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libhx509-5-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libkrb5-26-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libkrb5-26-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libheimntlm0-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libheimntlm0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../libgssapi3-heimdal_1.6~git20131207+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libgssapi3-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) over (1.6~git20120403+dfsg1-3ubuntu0.2) ... Preparing to unpack .../linux-libc-dev_3.13.0-10.30_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (3.13.0-10.30) over (3.13.0-8.28) ... Setting up libitm1:ppc64el (4.8.2-16ubuntu1) ... Setting up libgomp1:ppc64el (4.8.2-16ubuntu1) ... Setting up cpp-4.8 (4.8.2-16ubuntu1) ... Setting up gcc-4.8 (4.8.2-16ubuntu1) ... Setting up libatomic1:ppc64el (4.8.2-16ubuntu1) ... Setting up libgcc-4.8-dev:ppc64el (4.8.2-16ubuntu1) ... Setting up libstdc++-4.8-dev:ppc64el (4.8.2-16ubuntu1) ... Setting up g++-4.8 (4.8.2-16ubuntu1) ... Setting up libroken18-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libasn1-8-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libhcrypto4-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libheimbase1-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libwind0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libhx509-5-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libkrb5-26-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libheimntlm0-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up libgssapi3-heimdal:ppc64el (1.6~git20131207+dfsg-1ubuntu1) ... Setting up linux-libc-dev:ppc64el (3.13.0-10.30) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5604159', 'ppc64el', 'trusty', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty', '--purpose=PRIMARY', '--architecture=ppc64el', '--comp=universe', 'plink_1.07-3.dsc'] Initiating build PACKAGEBUILD-5604159 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-8-generic #28-Ubuntu SMP Tue Feb 11 17:58:07 UTC 2014 ppc64le Automatic build of plink_1.07-3 on denneed01 by sbuild/ppc64el 1.170.5 Build started at 20140219-1252 ****************************************************************************** plink_1.07-3.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), zlib1g-dev Checking for already installed source dependencies... debhelper: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof bsdmainutils dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.4 python3.4-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python3-doc python3-tk python3.4-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.4 python3.4-minimal zlib1g-dev 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 11.1 MB of archives. After this operation, 48.3 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1 ppc64el 2.1.0-4ubuntu1 [79.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main libmagic1 ppc64el 1:5.14-2ubuntu1 [194 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libssl1.0.0 ppc64el 1.0.1f-1ubuntu1 [762 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libasprintf0c2 ppc64el 0.18.3.1-1ubuntu2 [6748 B] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libglib2.0-0 ppc64el 2.39.4-0ubuntu1 [982 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 ppc64el 1.2.6-2 [22.6 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libxml2 ppc64el 2.9.1+dfsg1-3ubuntu3 [601 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main groff-base ppc64el 1.22.2-5 [1249 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils ppc64el 9.0.5ubuntu1 [173 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main man-db ppc64el 2.6.6-1 [847 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 ppc64el 0.6.8-2ubuntu1 [75.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libmpdec2 ppc64el 2.4.0-6 [83.9 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.4-minimal ppc64el 3.4~rc1-1build1 [440 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.4-stdlib ppc64el 3.4~rc1-1build1 [1972 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 ppc64el 0.9.3-5ubuntu3 [262 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main python3.4-minimal ppc64el 3.4~rc1-1build1 [1147 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main python3.4 ppc64el 3.4~rc1-1build1 [159 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main python3-minimal ppc64el 3.4~rc1-1 [23.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libpython3-stdlib ppc64el 3.4~rc1-1 [6976 B] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main python3 ppc64el 3.4~rc1-1 [8654 B] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main dh-python all 1.20140128-1ubuntu2 [51.0 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main file ppc64el 1:5.14-2ubuntu1 [19.2 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main gettext-base ppc64el 0.18.3.1-1ubuntu2 [47.2 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main gettext ppc64el 0.18.3.1-1ubuntu2 [840 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu38 [20.1 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu38 [7286 B] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main zlib1g-dev ppc64el 1:1.2.8.dfsg-1ubuntu1 [166 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.1 MB in 9s (1164 kB/s) Selecting previously unselected package libexpat1:ppc64el. (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.1.0-4ubuntu1) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu1_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.14-2ubuntu1) ... Selecting previously unselected package libssl1.0.0:ppc64el. Preparing to unpack .../libssl1.0.0_1.0.1f-1ubuntu1_ppc64el.deb ... Unpacking libssl1.0.0:ppc64el (1.0.1f-1ubuntu1) ... Selecting previously unselected package libasprintf0c2:ppc64el. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu2_ppc64el.deb ... Unpacking libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../libglib2.0-0_2.39.4-0ubuntu1_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.39.4-0ubuntu1) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../libpipeline1_1.2.6-2_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.2.6-2) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../libxml2_2.9.1+dfsg1-3ubuntu3_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.1+dfsg1-3ubuntu3) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-5_ppc64el.deb ... Unpacking groff-base (1.22.2-5) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5ubuntu1_ppc64el.deb ... Unpacking bsdmainutils (9.0.5ubuntu1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.6-1_ppc64el.deb ... Unpacking man-db (2.6.6-1) ... Selecting previously unselected package libcroco3:ppc64el. Preparing to unpack .../libcroco3_0.6.8-2ubuntu1_ppc64el.deb ... Unpacking libcroco3:ppc64el (0.6.8-2ubuntu1) ... Selecting previously unselected package libmpdec2:ppc64el. 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Preparing to unpack .../dh-apparmor_2.8.0-0ubuntu38_all.deb ... Unpacking dh-apparmor (2.8.0-0ubuntu38) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20131227ubuntu1_all.deb ... Unpacking debhelper (9.20131227ubuntu1) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1ubuntu1_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.8.dfsg-1ubuntu1) ... Setting up libexpat1:ppc64el (2.1.0-4ubuntu1) ... Setting up libmagic1:ppc64el (1:5.14-2ubuntu1) ... Setting up libssl1.0.0:ppc64el (1.0.1f-1ubuntu1) ... Setting up libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Setting up libglib2.0-0:ppc64el (2.39.4-0ubuntu1) ... No schema files found: doing nothing. Setting up libpipeline1:ppc64el (1.2.6-2) ... Setting up libxml2:ppc64el (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.6.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:ppc64el (0.6.8-2ubuntu1) ... Setting up libmpdec2:ppc64el (2.4.0-6) ... Setting up libpython3.4-minimal:ppc64el (3.4~rc1-1build1) ... Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython3.4-stdlib:ppc64el (3.4~rc1-1build1) ... Setting up libunistring0:ppc64el (0.9.3-5ubuntu3) ... Setting up python3.4-minimal (3.4~rc1-1build1) ... Setting up python3.4 (3.4~rc1-1build1) ... Setting up python3-minimal (3.4~rc1-1) ... Setting up libpython3-stdlib:ppc64el (3.4~rc1-1) ... Setting up file (1:5.14-2ubuntu1) ... Setting up gettext-base (0.18.3.1-1ubuntu2) ... Setting up gettext (0.18.3.1-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-1ubuntu1) ... Setting up python3 (3.4~rc1-1) ... running python rtupdate hooks for python3.4... running python post-rtupdate hooks for python3.4... Exception ignored in: > Traceback (most recent call last): File "/usr/lib/python3.4/subprocess.py", line 897, in __del__ TypeError: 'NoneType' object is not callable Setting up dh-python (1.20140128-1ubuntu2) ... Setting up apparmor-easyprof (2.8.0-0ubuntu38) ... Setting up dh-apparmor (2.8.0-0ubuntu38) ... Setting up debhelper (9.20131227ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.18-0ubuntu7 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu4 gcc-4.8_4.8.2-16ubuntu1 g++-4.8_4.8.2-16ubuntu1 binutils_2.24-2ubuntu3.1 libstdc++-4.8-dev_4.8.2-16ubuntu1 libstdc++6_4.8.2-16ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Mon Apr 23 08:26:19 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./plink_1.07-3.dsc dpkg-source: info: extracting plink in plink-1.07 dpkg-source: info: unpacking plink_1.07.orig.tar.gz dpkg-source: info: unpacking plink_1.07-3.debian.tar.gz dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-buildpackage: source package plink dpkg-buildpackage: source version 1.07-3 dpkg-buildpackage: source distribution unstable dpkg-source --before-build plink-1.07 dpkg-buildpackage: host architecture ppc64el /usr/bin/fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/plink-1.07' dh_auto_clean make[2]: Entering directory `/build/buildd/plink-1.07' rm -f *.o *~ make[2]: Leaving directory `/build/buildd/plink-1.07' rm -f plink make[1]: Leaving directory `/build/buildd/plink-1.07' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/plink-1.07' /usr/bin/make CXXFLAGS='-Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX' FORCE_DYNAMIC=1 make[2]: Entering directory `/build/buildd/plink-1.07' g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c plink.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ input.cpp: In member function 'void Plink::readData()': input.cpp:516:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( i == include.size() ) ^ input.cpp:521:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( i > include.size()) ^ input.cpp:545:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( gn != 2 * include.size() ) ^ input.cpp:579:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&, int&)': input.cpp:2116:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i sample.size()) ^ tinput.cpp:603:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( gn != 2 * sample.size() ) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c genome.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] int geno_nm = 0; ^ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] double tothet = 0; ^ genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^ genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] double e10 = E10*S; ^ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] double e20 = E20*S; ^ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] double e21 = E21*S; ^ genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( (!par::silent ) && c==c2 || c==np) ^ genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;isecond.size(); k++) ^ helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&)': helper.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&)': helper.cpp:100:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< m.size(); i++) ^ helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': helper.cpp:193:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int t=0; t > CArgs::value(std::string, int)': helper.cpp:267:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( (i+j) < a.size() ) ^ helper.cpp:277:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (r.size() != c) error("Not enough arguments given for option: "+s+" "); ^ helper.cpp: In function 'std::vector > parse2str(std::string)': helper.cpp:306:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0 ; i < s.length() ; i++) ^ helper.cpp:307:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (s[i] == ',' || i == s.length()-1 ) ^ helper.cpp:309:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (i == s.length()-1) t += s[i]; ^ helper.cpp: In function 'std::vector parse2int(std::string)': helper.cpp:323:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(h&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s = 0 ; s < snps.size() ; s++) ^ helper.cpp: In function 'std::string chromosomeName(int)': helper.cpp:952:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( c < 0 || c >= par::chr_code.size() ) ^ helper.cpp: In function 'int getMarkerChromosome(Plink&, std::string)': helper.cpp:959:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i getChromosomeRange(Plink&)': helper.cpp:1040:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i >)': helper.cpp:1172:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kfid.length() > par::pp_maxfid) ^ helper.cpp:1267:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (sample[i]->iid.length() > par::pp_maxiid) ^ helper.cpp:1273:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (locus[l]->name.length() > par::pp_maxsnp) ^ 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] for (int i=0; i&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i, Individual*>&)': helper.cpp:2935:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&)': helper.cpp:2959:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( input.size() != P.nl_all ) ^ helper.cpp: In function 'std::map, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] set * s; ^ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] int last = -1; ^ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] int thisChromosome = P.locus[0]->chr; ^ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] int nextChromosome; ^ 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] } ^ 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 '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 'double CArgs::value_double(std::string)': helper.cpp:256:1: 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 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 'double getDouble(std::string, std::string)': helper.cpp:407:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c stats.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^ 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] for (int c = 0 ; c < keep.size(); c++) ^ stats.cpp:1483:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ^ stats.cpp:1515:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ^ stats.cpp:1521:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ^ stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < v.size(); i++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0;isecond.size(); k++) ^ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=1; z<=qt.size(); z++) ^ cluster.cpp:452:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i >&, std::vector&, std::vector&)': cluster.cpp:1203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1228:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&)': cluster.cpp:1254:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&)': cluster.cpp:1272:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1290:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i1=0; i1second.size(); k++) ^ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 4; isecond.size(); k++) ^ 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] for (int i=0; iprofileSNPs.size(); i++) ^ assoc.cpp:741:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ^ assoc.cpp:744:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ^ assoc.cpp:785:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;ipv_set.size();i++) ^ assoc.cpp:788:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ^ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^ assoc.cpp: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': assoc.cpp:1109:70: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); ^ assoc.cpp:1019:14: note: 'pvalue' was declared here double pvalue; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c epi.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int e=0;esecond.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; i&)': phase.cpp:472:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (h&)': phase.cpp:1888:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0; z < h1.size(); z++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; ckid.size(); c++) ^ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kkid.size(); k++) ^ trio.cpp:272:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kkid.size(); k++) ^ trio.cpp:335:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ^ trio.cpp:342:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ^ trio.cpp:350:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ^ trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fkid.size(); c++) ^ trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteIndividuals(indel); ^ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fpm->kids.size(); k++) ^ trio.cpp:1245:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; kpp->kids.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iperson.size(); i++) ^ tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^ tdt.cpp:132:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fkid.size(); c++) ^ tdt.cpp:210:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ^ tdt.cpp:234:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fselectedSNPs[l].size(); j++) ^ tdt.cpp:330:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ^ tdt.cpp:412:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;ipv_set.size();i++) ^ tdt.cpp:415:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ^ 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] for (int f=0; fsecond.size(); k++) ^ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; lsecond.size(); k++) ^ 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] for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l >&, Set&, Plink&)': genepi.cpp:1025:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l&, 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] bool casewise_deletion = false; ^ genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:614:17: warning: 'cancor1_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] int cancor1_pos; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; i snpset[i].size() ) ^ sets.cpp:62:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (par::set_max==-1 || par::set_max > snpset[i].size() ) ^ sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0;isecond.size(); k++) ^ perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j&, std::vector&)': perm.cpp:273:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0;j< P.pS->snpset[l].size();j++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c mh.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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kkids.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i include.size()) ^ merge.cpp:733:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( gn != 2 * include.size() ) ^ merge.cpp:784:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wmaybe-uninitialized] if (write) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c hotel.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if (!sample[i]->missing) ^ hotel.cpp:173:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; ssecond.size(); k++) ^ 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] for (int l=0; lsecond.size(); k++) ^ 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] for (int i=0; i&, int, bool)': haploCC.cpp:48:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ^ haploCC.cpp:62:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ^ haploCC.cpp:79:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ^ haploCC.cpp:93:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ^ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); ^ haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ^ haploCC.cpp:357:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ^ haploCC.cpp:375:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ^ haploCC.cpp:392:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ 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] for (int f=0; fpv_set.size();i++) ^ poo.cpp:198:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ^ 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] for (int f=0; fsecond.size(); k++) ^ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ^ qfam.cpp:89:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ^ qfam.cpp:97:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ^ qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < family.size(); i++) ^ qfam.cpp:315:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f = 0 ; f < family.size() ; f++) ^ 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] for ( int k = 0 ; k < (*f)->kid.size() ; k++) ^ qfam.cpp:648:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] long int inc; ^ bmerge.cpp:357:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond; ^ bmerge.cpp:697:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (ssecond.size(); k++) ^ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without void setOptions(CArgs & a) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; ihap1[i].size(); z++) ^ mishap.cpp:236:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ^ mishap.cpp:349:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ^ mishap.cpp:373:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ^ homozyg.cpp:695:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ^ homozyg.cpp:722:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ^ homozyg.cpp:756:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ^ homozyg.cpp:773:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ^ homozyg.cpp:861:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ^ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ^ homozyg.cpp:1178:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ^ homozyg.cpp:1331:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< (*pA)->segs.size(); i++) ^ homozyg.cpp:1437:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ^ homozyg.cpp:1441:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( (*pA)->match[i].size() >= maxlist ) ^ homozyg.cpp:1461:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ^ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:20: warning: value computed is not used [-Wunused-value] homozygWindows[l] == 0; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:15: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^ segment.cpp:955:15: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^ segment.cpp:1027:19: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^ segment.cpp:1028:19: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] int c=0; ^ segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;ifirst; ^ segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] int nseg = smap.size(); ^ segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ^ segment.cpp:2380:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ^ segment.cpp:2382:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ^ segment.cpp:2412:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ^ segment.cpp:2414:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ^ segment.cpp:2416:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ^ segment.cpp:2443:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ^ segment.cpp:2445:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ^ segment.cpp:2447:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ^ segment.cpp:2474:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ^ segment.cpp:2476:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ^ segment.cpp:2478:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; i&)': model.cpp:132:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( include.size() != P->n ) ^ model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< par::parameter_list.size(); i++) ^ model.cpp:367:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0 ; i < X.size() ; i++) ^ model.cpp:374:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < par::parameter_list.size() ; j++) ^ model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] double maxVIF = 0; ^ 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 -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; icurrent->group.size(); h++) ^ glm.cpp:344:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; c *xn)) goto S160; ^ dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ^ 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] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ^ dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ^ dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ^ dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; ^ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ^ elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l< original.size(); l++) ^ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] const double pthresh = 0.01; ^ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] bool one_sided = true; ^ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] int srange_cnt = 0; ^ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] bool inRange = false; ^ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++) ^ elf.cpp:939:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( tokens.size() != ncol ) ^ elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:400:48: warning: 'wt' may be used uninitialized in this function [-Wmaybe-uninitialized] r[i] += par::rare_test_weight1 ? wt : 1 ; ^ In file included from elf.cpp:18:0: plink.h: In member function 'void Plink::displayRareRange()': plink.h:135:16: warning: 'srange.Range::stop' may be used uninitialized in this function [-Wmaybe-uninitialized] stop = p3; ^ elf.cpp:986:9: note: 'srange.Range::stop' was declared here Range srange; ^ In file included from elf.cpp:18:0: plink.h:133:15: warning: 'srange.Range::chr' may be used uninitialized in this function [-Wmaybe-uninitialized] chr = p1; ^ elf.cpp:986:9: note: 'srange.Range::chr' was declared here Range srange; ^ In file included from elf.cpp:18:0: plink.h:134:17: warning: 'srange.Range::start' may be used uninitialized in this function [-Wmaybe-uninitialized] start = p2; ^ elf.cpp:986:9: note: 'srange.Range::start' was declared here Range srange; ^ elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1142:19: warning: 'p_gcnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_gcnt); ^ elf.cpp:1165:15: warning: 'p_cnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_cnt); ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int f=0; fkid.size(); k++) ^ dfam.cpp:96:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; kkid.size(); k++) ^ dfam.cpp:106:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; cperson.size(); c++) ^ dfam.cpp:157:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fkid.size(); c++) ^ dfam.cpp:378:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; ckid.size(); c++) ^ dfam.cpp:218:9: warning: unused variable 'informative' [-Wunused-variable] bool informative = false; ^ dfam.cpp:504:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; cperson.size(); c++) ^ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] int totalInformative = 0; ^ dfam.cpp:247:13: warning: 'homozygParent' may be used uninitialized in this function [-Wmaybe-uninitialized] bool homozygParent; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ 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] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:501:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ 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] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(20, "This should never occur."); ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l< locus.size(); l++) ^ linput.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] char out_buf[BUF_SIZE+1]; // Output buffer for GET request ^ sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] char in_buf[BUF_SIZE+1]; // Input buffer for response ^ sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] unsigned int i; // Loop counter ^ sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] int echoStringLen = 100; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=25; isecond.size(); k++) ^ 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] for (int i=0; i= par::proxy_snp_filter ) ^ proxy.cpp:854:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ^ proxy.cpp:1332:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ^ proxy.cpp:1401:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c1 = 0; c1 < collection.size() ; c1++ ) ^ proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] int t1=0; ^ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] CSNP * s = SNP[l]; ^ proxy.cpp:936:4: warning: 'ref' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( s == ref ) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; i&, int, bool)': haploQTL.cpp:83:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ^ haploQTL.cpp:145:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; i > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int h=0; h&)': haplohelper.cpp:1419:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ^ haplohelper.cpp:1477:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ^ haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0; z < windows[w]->hap1[r].size(); z++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; iwindows[w]->hap1[r].size(); z++) ^ haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (hsecond.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; i&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] double posterior = ip->second; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; i clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; flocus.size()-1 ) ^ clumpld.cpp:520:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ^ clumpld.cpp:611:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ^ clumpld.cpp:1097:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( j < grouped_snps.size()-1) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; ihap1[i].size(); z++) ^ impute.cpp:161:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=0; z< currentWindow->pp[i].size(); z++) ^ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) ^ impute.cpp:313:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s < g.size(); s++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; ^ profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] bool OLD_clist = par::clist; ^ profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^ profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^ profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^ profile.cpp:390:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] bool a1 = i2->second; ^ profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] bool sawNamedAllele = false; ^ profile.cpp:629:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; lsecond.size(); k++) ^ 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] for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i > NList::tokenize(std::string)': nlist.cpp:189:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); k++) ^ 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] for (int i=0; ins + H->nh ) ^ whap.cpp:1129:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< lst.size(); i++) ^ whap.cpp:1142:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iconditioner.size(); c++) ^ whap.cpp:1334:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l&, ChapModel&)': whap.cpp:1389:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0;l0 && cnt2 < m.group[h].size() ) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c simul.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] double gh_11_12 = h11*h12; ^ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; ssecond.size(); k++) ^ gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; lsecond; ^ gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] bool fatal = false; ^ gvar.cpp:549:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; lsecond.size(); k++) ^ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:8: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^ cnv.cpp:247:11: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^ cnv.cpp:332:12: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^ cnv.cpp:332:15: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^ cnv.cpp:815:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s1=0; s1&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < scaffold.size(); c++) ^ cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] noCovar == true; ^ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] indivPair p = ic->first; ^ cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^ cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^ cnv.cpp: In member function 'void Plink::processCNVList()': cnv.cpp:1500:13: warning: 'cdet.CInfo::lstart' may be used uninitialized in this function [-Wmaybe-uninitialized] CInfo cdet; ^ cnv.cpp:1500:13: warning: 'cdet.CInfo::lstop' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond.size(); l+=2) ^ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] long int nfound = 0; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ^ cfamily.cpp:221:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ^ cfamily.cpp:237:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ^ cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ^ cfamily.cpp:276:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ^ cfamily.cpp:288:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c setscreen.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] for ( int k = 0 ; k < i->second.size(); k++) ^ setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isnpset.size(); j++ ) ^ setscreen.cpp:196:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < snpset[j].size(); i++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c idhelp.cpp 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] for (int k=0; ksecond.size(); k++) ^ 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] for ( int i = 0 ; i < ids.size() ; i++) ^ idhelp.cpp:63:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&)': idhelp.cpp:136:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int g=0; gvalues.size(); g++) ^ idhelp.cpp:169:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( found != matchTemplate.size() ) ^ idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] bool match = true; ^ idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ^ idhelp.cpp:221:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ^ idhelp.cpp:296:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0 ; i < mask.size() ; i++) ^ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] vector & jo = jointOrder[j]; ^ 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] for ( int g = 0 ; g < idgroup.size(); g++ ) ^ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ++p == tokens.size() ) ^ idhelp.cpp:510:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( p < tokens.size() ) ^ idhelp.cpp:542:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ^ idhelp.cpp:547:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ^ idhelp.cpp:553:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ^ idhelp.cpp:529:10: warning: unused variable 'seenJoint' [-Wunused-variable] bool seenJoint = true; ^ idhelp.cpp:584:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ^ idhelp.cpp:594:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ^ idhelp.cpp:678:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ++p == tokens.size() ) ^ idhelp.cpp:727:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ^ idhelp.cpp:742:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ^ idhelp.cpp:745:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ^ idhelp.cpp:747:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ^ idhelp.cpp:757:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ^ idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] set & jf = jointField[j]; ^ idhelp.cpp:772:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ^ idhelp.cpp:790:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ^ idhelp.cpp:794:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ^ idhelp.cpp:808:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++) ^ idhelp.cpp:836:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k = 0 ; k < i->second.size(); k++) ^ idhelp.cpp:888:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( tokens.size() != file->uniqFieldCount ) ^ idhelp.cpp:894:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; ^ idhelp.cpp:903:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( j < tokens.size() ) ^ idhelp.cpp:922:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ^ idhelp.cpp:950:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i=0; ivalue.size() + 3 > myField->width ) ^ idhelp.cpp:1000:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ^ idhelp.cpp:1003:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ^ idhelp.cpp:1013:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ^ idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] IDGroup * group = idgroup[g]; ^ idhelp.cpp:1025:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ^ idhelp.cpp:1028:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ^ idhelp.cpp:1031:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1070:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ^ idhelp.cpp:1085:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ^ idhelp.cpp:1110:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ^ idhelp.cpp:1128:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0; k < (*i0)->values.size(); k++) ^ idhelp.cpp:1183:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=0; zvalues.size(); z++) ^ idhelp.cpp:1189:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=0; z<(*i0)->values.size(); z++) ^ idhelp.cpp:1236:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ^ idhelp.cpp:1242:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ^ idhelp.cpp:1245:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1346:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; ivalues.size(); j++ ) ^ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i=0; ivalues.size(); i++) ^ idhelp.cpp:1770:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i= tok.size() ) ^ idhelp.cpp:2034:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fvalues.size(); v++) ^ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] bool jointQuery = id.find("+") != string::npos; ^ idhelp.cpp:2167:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kvalues.size(); j++ ) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; isecond.size(); k++) ^ lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ^ lookup2.cpp:203:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ^ lookup2.cpp:280:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ^ lookup2.cpp:325:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int t = 0 ; t < tokens.size() ; t++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] int nsnps = toPosition - fromPosition + 1; ^ blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] int numStrong = 0; ^ blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] int numRec = 0; ^ blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] int numInGroup = 0; ^ blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^ blox.cpp:418:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; k0 ) loglike1 += knownBB * log( pB2 ); ^ blox.cpp:505:21: warning: 'pB1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^ blox.cpp:503:21: warning: 'pA2' may be used uninitialized in this function [-Wmaybe-uninitialized] double pA = pA1 + pA2; ^ blox.cpp:510:26: warning: 'pA1' may be used uninitialized in this function [-Wmaybe-uninitialized] double D = pA1 - (pA*p1); ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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] for ( int k = 0 ; k < i->second.size(); k++) ^ 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] for (int i=0; igetStatistic() : 0; ^ dosage.cpp:1252:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( o->second != dosageFilename_all.size() ) ^ dosage.cpp:1310:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ++qq == qthresh.size() ) ^ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] int geno_field = a2_field + skip2 + 1; ^ dosage.cpp:915:21: warning: 'snp_code' may be used uninitialized in this function [-Wmaybe-uninitialized] SNP[snp_code]->one[personPosition[f][i]] = s1; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c annot.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ^ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=1; jsecond.size(); k++) ^ 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] int bp; ^ metaanal.cpp:44:10: warning: 'std::string Alleles::a1' [-Wreorder] string a1; ^ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] Alleles(string name, int chr, int bp, string a1, string a2) ^ metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fsecond.size(); k++) ^ In file included from r.cpp:29:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } ^ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ^ Rconnection.h:249:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < nel) { ^ r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] int ct = data->length(); ^ r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rCov; ^ r.cpp:378:14: warning: 'rS' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rS; ^ r.cpp:377:14: warning: 'rP' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rP; ^ r.cpp:376:14: warning: 'rN' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rN; ^ r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rc; ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c Rconnection.cpp In file included from Rconnection.cpp:30:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } ^ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ^ Rconnection.h:249:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < nel) { ^ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ ^ g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c zfstream.cpp g++ -Wall -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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[2]: Leaving directory `/build/buildd/plink-1.07' make[1]: Leaving directory `/build/buildd/plink-1.07' dh_auto_test -a /usr/bin/fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory `/build/buildd/plink-1.07' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory `/build/buildd/plink-1.07' dh_installman -a dh_perl -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: plink dh_strip debug symbol extraction: packages to act on: plink dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `plink-dbgsym' in `../plink-dbgsym_1.07-3_ppc64el.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 119 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 pkgstripfiles: PNG optimization for package plink took 0 s 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_1.07-3_ppc64el.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../plink_1.07-3_ppc64el.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 20140219-1300 Publishing debug debs. chroot-autobuild/build/buildd/plink_1.07-3_ppc64el.deb: new debian package, version 2.0. size 1031112 bytes: control archive=1104 bytes. 1123 bytes, 26 lines control 534 bytes, 8 lines md5sums Package: plink Version: 1.07-3 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3481 Depends: libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), 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_1.07-3_ppc64el.deb: drwxr-xr-x root/root 0 2014-02-19 13:00 ./ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/bin/ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/lib/ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/lib/plink/ -rwxr-xr-x root/root 3507200 2014-02-19 13:00 ./usr/lib/plink/plink drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/share/ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/share/man/ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/share/man/man1/ -rw-r--r-- root/root 672 2014-02-19 13:00 ./usr/share/man/man1/p-link.1.gz drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/share/doc/plink/ -rw-r--r-- root/root 2204 2012-04-23 02:56 ./usr/share/doc/plink/copyright -rw-r--r-- root/root 1287 2007-07-27 10:51 ./usr/share/doc/plink/README.txt drwxr-xr-x root/root 0 2014-02-19 13:00 ./usr/share/doc/plink/examples/ -rw-r--r-- root/root 138 2007-07-27 10:51 ./usr/share/doc/plink/examples/test.ped -rw-r--r-- root/root 23 2007-07-27 10:51 ./usr/share/doc/plink/examples/test.map -rw-r--r-- root/root 1406 2012-04-23 04:22 ./usr/share/doc/plink/changelog.Debian.gz -rw-r--r-- root/root 1590 2009-04-30 16:38 ./usr/share/doc/plink/README.Debian lrwxrwxrwx root/root 0 2014-02-19 13:00 ./usr/bin/p-link -> ../lib/plink/plink plink_1.07-3_ppc64el.changes: Format: 1.8 Date: Mon, 23 Apr 2012 07:23:07 +0000 Source: plink Binary: plink Architecture: ppc64el Version: 1.07-3 Distribution: trusty Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Andreas Tille Description: plink - whole-genome association analysis toolset Closes: 667325 Changes: plink (1.07-3) unstable; urgency=low . * debian/patches/gcc-4.7.patch: previous patch was incomplete because the same problem occured in more files. Now really Closes: #667325 Checksums-Sha1: cce08403259b6fdb8a08678bf657ca2577bd6b96 1031112 plink_1.07-3_ppc64el.deb Checksums-Sha256: 7342ccceec6e5cd5ccbd93bfd1b2e589797e54c0d155235375802903573d8e79 1031112 plink_1.07-3_ppc64el.deb Files: ab1b8f3631e5c7cfc23536b10dab963c 1031112 science optional plink_1.07-3_ppc64el.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20140219-1300 Build needed 00:07:50, 252588k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5604159'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5604159/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5604159'] Unmounting chroot for build PACKAGEBUILD-5604159... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5604159'] Removing build PACKAGEBUILD-5604159